i couldn't create a test case. but while debugging i've noticed that FrameBuffer.clearColorBufferOnly results in a call to glClear, may this be relavant?
below are the logs of a whole cycle. it starts with FrameBuffer.clear which calls glClearColor and glClear. in the middle, there is a call to FrameBuffer.clearColorBufferOnly which also calls glClearColor and glClear.
FrameBuffer.clear(color)
02-20 11:36:20.374: I/jPCT-AE(14432): glClearColor(0.0, 0.0, 0.0, 1.0) took 86041ns
02-20 11:36:20.374: I/jPCT-AE(14432): glClear(16640) took 462666ns
02-20 11:36:35.979: I/jPCT-AE(14432): glMatrixMode(5889) took 272125ns
02-20 11:36:35.984: I/jPCT-AE(14432): glLoadIdentity() took 309584ns
02-20 11:36:35.994: I/jPCT-AE(14432): glFrustumf(-0.625, 0.625, -0.3515625, 0.3515625, 1.0, 15000.0) took 368125ns
02-20 11:36:35.999: I/jPCT-AE(14432): glDisable(2912) took 294541ns
02-20 11:36:36.004: I/jPCT-AE(14432): glEnable(2977) took 290709ns
02-20 11:36:36.004: I/jPCT-AE(14432): glEnable(2896) took 289958ns
02-20 11:36:36.009: I/jPCT-AE(14432): glEnable(2884) took 494709ns
02-20 11:36:36.009: I/jPCT-AE(14432): glEnable(3042) took 333292ns
02-20 11:36:36.014: I/jPCT-AE(14432): glBlendFunc(770, 771) took 310209ns
02-20 11:36:36.014: I/jPCT-AE(14432): glDepthMask(false) took 287791ns
02-20 11:36:36.019: I/jPCT-AE(14432): glActiveTexture(33984) took 297959ns
02-20 11:36:36.024: I/jPCT-AE(14432): glBindTexture(3553, 4) took 303916ns
02-20 11:36:36.024: I/jPCT-AE(14432): glMatrixMode(5888) took 256666ns
02-20 11:36:36.029: I/jPCT-AE(14432): glPushMatrix() took 323542ns
02-20 11:36:36.029: I/jPCT-AE(14432): glLoadIdentity() took 287708ns
02-20 11:36:36.034: I/jPCT-AE(14432): glLightModelfv(2899, [F@424d4f40, 0) took 270166ns
02-20 11:36:36.039: I/jPCT-AE(14432): glMaterialfv(1032, 5632, [F@424d4f68, 0) took 277041ns
02-20 11:36:36.039: I/jPCT-AE(14432): glLoadMatrixf([F@4248e6b8, 0) took 287666ns
02-20 11:36:36.044: I/jPCT-AE(14432): glEnableClientState(32885) took 292875ns
02-20 11:36:36.049: I/jPCT-AE(14432): glBindBuffer(34962, 1) took 633375ns
02-20 11:36:36.049: I/jPCT-AE(14432): glNormalPointer(5132, 12, 0) took 74458ns
02-20 11:36:36.054: I/jPCT-AE(14432): glEnableClientState(32884) took 181459ns
02-20 11:36:36.054: I/jPCT-AE(14432): glBindBuffer(34962, 2) took 84708ns
02-20 11:36:36.054: I/jPCT-AE(14432): glVertexPointer(3, 5132, 12, 0) took 80708ns
02-20 11:36:36.054: I/jPCT-AE(14432): glDisableClientState(32886) took 97875ns
02-20 11:36:36.054: I/jPCT-AE(14432): glClientActiveTexture(33984) took 74625ns
02-20 11:36:36.054: I/jPCT-AE(14432): glEnableClientState(32888) took 84666ns
02-20 11:36:36.054: I/jPCT-AE(14432): glBindBuffer(34962, 3) took 75875ns
02-20 11:36:36.059: I/jPCT-AE(14432): glTexCoordPointer(2, 5132, 8, 0) took 86292ns
02-20 11:36:36.059: I/jPCT-AE(14432): glBindBuffer(34962, 0) took 73792ns
02-20 11:36:36.059: I/jPCT-AE(14432): glBindBuffer(34963, 4) took 74333ns
02-20 11:36:36.059: I/jPCT-AE(14432): glDrawElements(4, 48, 5123, 0) took 127750ns
02-20 11:36:36.059: I/jPCT-AE(14432): glBindBuffer(34963, 0) took 75625ns
02-20 11:36:36.059: I/jPCT-AE(14432): glMatrixMode(5888) took 64958ns
02-20 11:36:36.064: I/jPCT-AE(14432): glPopMatrix() took 74791ns
02-20 11:36:36.064: I/jPCT-AE(14432): glDisable(3042) took 85083ns
02-20 11:36:36.064: I/jPCT-AE(14432): glDepthMask(true) took 72542ns
02-20 11:36:36.064: I/jPCT-AE(14432): glDisable(2884) took 81458ns
02-20 11:36:36.064: I/jPCT-AE(14432): glDisable(2896) took 71917ns
02-20 11:36:36.064: I/jPCT-AE(14432): glDisable(2977) took 73959ns
FrameBuffer.clearColorBufferOnly(color)
02-20 11:36:36.064: I/jPCT-AE(14432): glClearColor(0.0, 0.0, 0.0, 1.0) took 76292ns
02-20 11:36:36.069: I/jPCT-AE(14432): glClear(16384) took 93917ns
and the rest:
02-20 11:36:44.644: I/jPCT-AE(14432): glDisable(2929) took 365833ns
02-20 11:36:44.649: I/jPCT-AE(14432): glDeleteTextures(1, java.nio.IntToByteBufferAdapter, status: capacity=1 position=0 limit=1) took 443000ns
02-20 11:36:44.654: I/jPCT-AE(14432): glGenTextures(1, java.nio.IntToByteBufferAdapter, status: capacity=1 position=0 limit=1) took 445417ns
02-20 11:36:44.654: I/jPCT-AE(14432): glActiveTexture(33984) took 302959ns
02-20 11:36:44.659: I/jPCT-AE(14432): glBindTexture(3553, 2) took 326500ns
02-20 11:36:44.664: I/jPCT-AE(14432): glTexParameterx(3553, 10241, 9729) took 694001ns
02-20 11:36:44.669: I/jPCT-AE(14432): glTexParameterx(3553, 10240, 9729) took 361792ns
02-20 11:36:44.669: I/jPCT-AE(14432): glTexParameterx(3553, 10242, 10497) took 372167ns
02-20 11:36:44.674: I/jPCT-AE(14432): glTexParameterx(3553, 10243, 10497) took 80792ns
02-20 11:36:44.679: I/jPCT-AE(14432): glTexImage2D(3553, 0, 6408, 512, 512, 0, 6408, 5121, java.nio.ReadWriteHeapByteBuffer, status: capacity=1048576 position=0 limit=1048576) took 1882959ns
02-20 11:36:44.679: I/jPCT-AE(14432): glBindTexture(3553, -1) took 83875ns
02-20 11:36:44.679: I/jPCT-AE(14432): glBindTexture(3553, 2) took 77334ns
02-20 11:36:50.324: I/jPCT-AE(14432): glVertexPointer(3, 5132, 12, java.nio.IntToByteBufferAdapter, status: capacity=1800 position=0 limit=1800) took 397583ns
02-20 11:36:50.324: I/jPCT-AE(14432): glEnableClientState(32884) took 86833ns
02-20 11:36:50.324: I/jPCT-AE(14432): glDisableClientState(32885) took 74458ns
02-20 11:36:50.324: I/jPCT-AE(14432): glClientActiveTexture(33984) took 77291ns
02-20 11:36:50.324: I/jPCT-AE(14432): glEnableClientState(32888) took 256542ns
02-20 11:36:50.329: I/jPCT-AE(14432): glTexCoordPointer(2, 5132, 8, java.nio.IntToByteBufferAdapter, status: capacity=1200 position=0 limit=1200) took 106333ns
02-20 11:36:50.329: I/jPCT-AE(14432): glColorPointer(4, 5132, 16, java.nio.IntToByteBufferAdapter, status: capacity=2400 position=0 limit=2400) took 97000ns
02-20 11:36:50.329: I/jPCT-AE(14432): glEnableClientState(32886) took 103041ns
02-20 11:36:50.329: I/jPCT-AE(14432): glDrawElements(4, 6, 5123, java.nio.ShortToByteBufferAdapter, status: capacity=1200 position=0 limit=1200) took 137083ns
02-20 11:36:50.329: I/jPCT-AE(14432): glEnable(2929) took 92708ns
02-20 11:36:50.334: I/jPCT-AE(14432): glMatrixMode(5889) took 73083ns
02-20 11:36:50.334: I/jPCT-AE(14432): glLoadIdentity() took 85333ns
02-20 11:36:50.334: I/jPCT-AE(14432): glFrustumf(-0.625, 0.625, -0.3515625, 0.3515625, 1.0, 15000.0) took 86708ns
02-20 11:36:50.334: I/jPCT-AE(14432): glDisable(2912) took 73500ns
02-20 11:36:50.339: I/jPCT-AE(14432): glEnable(2977) took 73583ns
02-20 11:36:50.339: I/jPCT-AE(14432): glEnable(2896) took 890208ns
02-20 11:36:50.339: I/jPCT-AE(14432): glEnable(2884) took 91125ns
02-20 11:36:50.339: I/jPCT-AE(14432): glActiveTexture(33984) took 76584ns
02-20 11:36:50.344: I/jPCT-AE(14432): glBindTexture(3553, 5) took 78875ns
02-20 11:36:50.344: I/jPCT-AE(14432): glMatrixMode(5888) took 65291ns
02-20 11:36:50.344: I/jPCT-AE(14432): glPushMatrix() took 59666ns
02-20 11:36:50.344: I/jPCT-AE(14432): glLoadIdentity() took 72958ns
02-20 11:36:50.344: I/jPCT-AE(14432): glLightModelfv(2899, [F@424d4f40, 0) took 67042ns
02-20 11:36:50.344: I/jPCT-AE(14432): glMaterialfv(1032, 5632, [F@424d4f68, 0) took 67708ns
02-20 11:36:50.349: I/jPCT-AE(14432): glLoadMatrixf([F@4248e6b8, 0) took 72083ns
02-20 11:36:50.349: I/jPCT-AE(14432): glEnableClientState(32885) took 73500ns
02-20 11:36:50.349: I/jPCT-AE(14432): glBindBuffer(34962, 5) took 77625ns
02-20 11:36:50.349: I/jPCT-AE(14432): glNormalPointer(5132, 12, 0) took 65292ns
02-20 11:36:50.349: I/jPCT-AE(14432): glEnableClientState(32884) took 84958ns
02-20 11:36:50.349: I/jPCT-AE(14432): glBindBuffer(34962, 6) took 76000ns
02-20 11:36:50.354: I/jPCT-AE(14432): glVertexPointer(3, 5132, 12, 0) took 81458ns
02-20 11:36:50.354: I/jPCT-AE(14432): glDisableClientState(32886) took 94874ns
02-20 11:36:50.354: I/jPCT-AE(14432): glClientActiveTexture(33984) took 74333ns
02-20 11:36:50.354: I/jPCT-AE(14432): glEnableClientState(32888) took 83583ns
02-20 11:36:50.354: I/jPCT-AE(14432): glBindBuffer(34962, 7) took 74875ns
02-20 11:36:50.354: I/jPCT-AE(14432): glTexCoordPointer(2, 5132, 8, 0) took 86167ns
02-20 11:36:50.354: I/jPCT-AE(14432): glBindBuffer(34962, 0) took 74250ns
02-20 11:36:50.359: I/jPCT-AE(14432): glBindBuffer(34963, 8) took 74959ns
02-20 11:36:50.359: I/jPCT-AE(14432): glDrawElements(4, 36, 5123, 0) took 113833ns
02-20 11:36:50.359: I/jPCT-AE(14432): glBindBuffer(34963, 0) took 75250ns
02-20 11:36:50.359: I/jPCT-AE(14432): glMatrixMode(5888) took 63834ns
02-20 11:36:50.359: I/jPCT-AE(14432): glPopMatrix() took 73084ns
02-20 11:36:50.359: I/jPCT-AE(14432): glEnable(3042) took 83750ns
02-20 11:36:50.359: I/jPCT-AE(14432): glBlendFunc(770, 771) took 76458ns
02-20 11:36:50.364: I/jPCT-AE(14432): glDepthMask(false) took 73500ns
02-20 11:36:50.364: I/jPCT-AE(14432): glActiveTexture(33984) took 72417ns
02-20 11:36:50.364: I/jPCT-AE(14432): glBindTexture(3553, 4) took 75958ns
02-20 11:36:50.364: I/jPCT-AE(14432): glMatrixMode(5888) took 65208ns
02-20 11:36:50.364: I/jPCT-AE(14432): glPushMatrix() took 58709ns
02-20 11:36:50.364: I/jPCT-AE(14432): glLoadIdentity() took 72916ns
02-20 11:36:50.364: I/jPCT-AE(14432): glLightModelfv(2899, [F@424d4f40, 0) took 66625ns
02-20 11:36:50.369: I/jPCT-AE(14432): glMaterialfv(1032, 5632, [F@424d4f68, 0) took 67750ns
02-20 11:36:50.369: I/jPCT-AE(14432): glLoadMatrixf([F@4248e6b8, 0) took 72208ns
02-20 11:36:50.369: I/jPCT-AE(14432): glEnableClientState(32885) took 72791ns
02-20 11:36:50.369: I/jPCT-AE(14432): glBindBuffer(34962, 9) took 75083ns
02-20 11:36:50.369: I/jPCT-AE(14432): glNormalPointer(5132, 12, 0) took 65000ns
02-20 11:36:50.369: I/jPCT-AE(14432): glEnableClientState(32884) took 83459ns
02-20 11:36:50.374: I/jPCT-AE(14432): glBindBuffer(34962, 10) took 76166ns
02-20 11:36:50.374: I/jPCT-AE(14432): glVertexPointer(3, 5132, 12, 0) took 78750ns
02-20 11:36:50.374: I/jPCT-AE(14432): glDisableClientState(32886) took 92417ns
02-20 11:36:50.374: I/jPCT-AE(14432): glClientActiveTexture(33984) took 73083ns
02-20 11:36:50.374: I/jPCT-AE(14432): glEnableClientState(32888) took 83625ns
02-20 11:36:50.374: I/jPCT-AE(14432): glBindBuffer(34962, 11) took 77667ns
02-20 11:36:50.379: I/jPCT-AE(14432): glTexCoordPointer(2, 5132, 8, 0) took 87709ns
02-20 11:36:50.379: I/jPCT-AE(14432): glBindBuffer(34962, 0) took 75541ns
02-20 11:36:50.379: I/jPCT-AE(14432): glBindBuffer(34963, 12) took 74834ns
02-20 11:36:50.379: I/jPCT-AE(14432): glDrawElements(4, 486, 5123, 0) took 103875ns
02-20 11:36:50.379: I/jPCT-AE(14432): glBindBuffer(34963, 0) took 74625ns
02-20 11:36:50.379: I/jPCT-AE(14432): glMatrixMode(5888) took 64334ns
02-20 11:36:50.384: I/jPCT-AE(14432): glPopMatrix() took 72417ns
02-20 11:36:50.384: I/jPCT-AE(14432): glDisable(3042) took 84875ns
02-20 11:36:50.384: I/jPCT-AE(14432): glDepthMask(true) took 71916ns
02-20 11:36:50.384: I/jPCT-AE(14432): glDisable(2884) took 81417ns
02-20 11:36:50.384: I/jPCT-AE(14432): glDisable(2896) took 72792ns
02-20 11:36:50.384: I/jPCT-AE(14432): glDisable(2977) took 72917ns
02-20 11:36:52.699: I/jPCT-AE(14432): glEnable(3042) took 361959ns
02-20 11:36:52.704: I/jPCT-AE(14432): glBlendFunc(770, 771) took 307500ns
02-20 11:36:52.704: I/jPCT-AE(14432): glDisable(2929) took 333209ns
02-20 11:36:52.709: I/jPCT-AE(14432): glActiveTexture(33984) took 296708ns
02-20 11:36:52.714: I/jPCT-AE(14432): glBindTexture(3553, 3) took 303500ns
02-20 11:36:55.839: I/jPCT-AE(14432): glVertexPointer(3, 5132, 12, java.nio.IntToByteBufferAdapter, status: capacity=1800 position=0 limit=1800) took 396500ns
02-20 11:36:55.844: I/jPCT-AE(14432): glEnableClientState(32884) took 339208ns
02-20 11:36:55.844: I/jPCT-AE(14432): glDisableClientState(32885) took 291333ns
02-20 11:36:55.849: I/jPCT-AE(14432): glClientActiveTexture(33984) took 301166ns
02-20 11:36:55.849: I/jPCT-AE(14432): glEnableClientState(32888) took 331292ns
02-20 11:36:55.859: I/jPCT-AE(14432): glTexCoordPointer(2, 5132, 8, java.nio.IntToByteBufferAdapter, status: capacity=1200 position=0 limit=1200) took 405750ns
02-20 11:36:55.864: I/jPCT-AE(14432): glColorPointer(4, 5132, 16, java.nio.IntToByteBufferAdapter, status: capacity=2400 position=0 limit=2400) took 380500ns
02-20 11:36:55.864: I/jPCT-AE(14432): glEnableClientState(32886) took 372917ns
02-20 11:36:55.869: I/jPCT-AE(14432): glDrawElements(4, 6, 5123, java.nio.ShortToByteBufferAdapter, status: capacity=1200 position=0 limit=1200) took 457542ns
02-20 11:36:55.874: I/jPCT-AE(14432): glDisable(3042) took 332375ns
02-20 11:36:55.879: I/jPCT-AE(14432): glEnable(2929) took 327458ns