If you conquer a planet and then use a planetary govenor queue with say 2 factories in it, and the planet already has one factory, the govenor will only build one more. Most of the time you can use the govenor safely. Only when you have tech tree differences are you liable to run into duplicates (two different buildings doing the same thing).
Since running the latest patch worked for me, maybe the next one will fix the problem (not very useful if you want to play now ). Other than that is it worth emailing help and finding out if there is any way to uninstall or reinstall the most recent patch? Worst case is unistalling Gal Civ, and reinstalling Gal Civ-> Hi-Res mod -> Latest patch. Sorry I can't be more helpful.
I too have experienced the problem of no bonus tiles on any world other than my homeworld (I am running the Hi-Res Graphic mod also). Having tried 5 new games and discovering all had the same problem, I was frustrated as it certainly removes a major element of interest to colonization. After trying all I could think of, I was considering a game reinstall. When I looked on Stardock Central I noticed I had missed one of the updates: Gal Civ II 1.50.098 dated 4/2/07. I installed that updat
GalCiv2 Forums