The only other built-in method for changing the color of the titles of some messages that I know of, besides a rule you might have built, is the Advanced Junk Mail Filter, but I think the default color for it is brown.
If that's not it, then we need some other input. Sorry, if that's not it then you'll probably want to repost your question with a title that says you want to remove colors from some message titles. That may get some attention with fewer questions about which colors you are talking about.