Reply #1 from Sins Forums Top
Make sure "use team colors" is disabled in Interface, and "Use mesh team colors" is enabled in Effects.

Also, all the patch beta feedback should go in the Beta Feedback forum :)
Reply #2 from Sins Forums Top
Beta Feedback forum. There's a couple of threads about colors, but they're a bit different.

EDIT: Argh, Annatar, argh.
Sins of a Solar Empire II
Reply #3 from Sins Forums Top
Haha, I talked to him on IRC too. :P