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The problem is in the j2d_glReadPixels() in OGLBlitLoop.c:

// we must read one scanline at a time because there is no way
// to read starting at the top-left corner of the source region
while (height > 0) {
j2d_glPixelStorei(GL_PACK_SKIP_ROWS, dsty);
j2d_glReadPixels(srcx, srcy, width, 1,
pf.format, pf.type, pDst);
srcy--;
dsty++;
height--;
}