OK, I've gotten some success here!
I updated from SVN, and after looking at the tweaks done to ufomap.exe (I read the SVN logs), I ran the .bat to compile maps with the /clean option, and after re-building the maps I think it worked - I went into Skirmish mode and tried several maps, the night versions, and although there were darker areas, I didn't get any squares that were completely black.
I really need to get to bed now, its late where I am, but tomorrow I'll try to remember to post a few screenshots.