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--;
            }