No idea then. Maybe there is some transformation stored in the file that jPCT's loader ignores. There are such things in 3DS, which is why the loader fails on some files. Maybe this is one of them. Try to convert it into OBJ-format and see if that helps.
If it doesn't, try to do something like:
mesh.getRotationMatrix().set(1,1,-1);
mesh.rotateMesh();
mesh.getRotationMatrix().setIdentity();
to flip y.