I haven't had a chance to look into this yet, but it definitely sounds like a bug. I try to maintain the color selections for each control mode independently (highlighting, drawing, text, etc), so it sounds like the code that switches the color selection is also switching the selected annotation color. Just for reference, if you want to change the color of an existing annotation, you can just select it, and then change the color selection at the bottom of the screen. The same logic that drives the color switching is being triggered when you switch control modes, so it should be easy to track and fix this bug.
Mike
Mike