that sounds like there is an endian issue in loading or saving the lightmap data - because they are calculated on a little endian system
Ok, where in ufo is the lightmap data read in, and what values should be seen? Do the lightmap values change as you rotate the map? (What's displayed does change as the map is rotated, and sometimes on a per-frame toggle.)
Lets see if we can get some debugging patches, and then see what values are read/used on ppc/x86.
Oh yea -- Local compiled farm maps are "mostly good" with minor issues, and the rare, occasional good.