When there was trouble with megaglest, I looked at the windows version of glest too.
I saw two big differences:
1. Nights are much much darker in windows glest with the same setting !?!
2. loading speed in windows is ultra slow compared to linux. I think linux loads a game 10 times faster ( I don't know if GAE is affected too because it uses another xml-parser )
Why are there these differences?