Strange then...it's this line that crashes:
myObj.multiTex[i][polyID] == TextureManager.TEXTURE_NOTFOUND
polyID is 0 in your case, so it can't be the problem. The length of multiTex should be maxTextureLayers-1, so if it crashes on index 1, it seems to me that the array has been created for only 2 texture layers. However, it's actually not supposed to crash...i've updated the beta jar with a version that should not crash but give a log output instead if it can't add another layer. It would be interesting to see what this prints out in your case.