OK dont know exactly what happened, but after a turn I noticed that the social, reasearch, and military productions were all screwed. You can focus on one, and the other 2 go to 0. If you dont set a focus then they all go to 0. Included a screenshot:
http://www.kommi.com/galciv2/colonyBug.jpg
and the save
http://www.kommi.com/galciv2/colonyBug.sav