Ok so I discovered that civ wide bonuses from improvements aren't posting (Even after loading save game) in the civ report screen that shows percentage.  Also things that should be viewable immediatly in the colony screen such as morale or research trade goods don't appear to do anything.  I'll not send a save game because this is easily reproducable start with korx and rush buy galactic bazaar.  I am using metaverse copy of planet improvements xml file.  I am using a custom race that already has bonuses in each area (econ, research, trade) but I tried to do it with korx and it didn't work there either (because they can build bazaar right off).

Got another bug that is slightly more work to reproduce I'll make a seperate post for that.