[theOZer]

Are you testing this using different 'test' people. I have different psuedo users that I log in as, one's a SuperMod, one's a Regular User, one's a Mod, and my Admin user.
And, you're right. It does appear that the Team channel only uses the default color (not a user's preferences) for, say, Team channel. Try putzing with that color if nothing else. In each usergroup there's a 'MGC Chatbox Evo: Default chat color.' Tweak that, see, if nothing else, if that has any affect.
Regards, ~OZ