Ok, I made some changes to my lighter plugin and now it supports '3do-style' lighting, where surfaces facing the light will be lit more than those facing away. It's also a little faster now.
I couldn't fix the problem with your level though...but I think that the issue you are having with consistency problems (and probably what breaks my plugin) might be due to inaccuracies that show up from saving levels in text files (.jkl, .jed). Everything looks *almost* perfect when looking at it in jed, but you can see where things get very slightly off. Your level is pretty big, and the difference between something being convex/concave and overlapping vs lining up just right is pretty small, so that could be what is going wrong. If there's some plugin or function in jed for 'welding' vertices that are very close into one, that might help a bit.
The new version of the plugin is here:
http://www.txstate.edu/~an1047/lighter.zip
I'll try to get the one on jkhub replaced with this soon.