I've been curious about that too..
There was a post not too long ago concerning issues that seem to be related to My Colors....
linkPoster already had apps (WB, etc) installed and got skin errors changing from MC to WB... uninstalling MC cleared up the WB issue.
I'm thinking it might be along the lines of AlienGuise vs Thememgr - caused issues for some. When I downloaded AG I seem to recall getting a prompt about 'you seem to have SD TM installed, etc., do you wish to keep that as the default?'