I've never heared of anything like this before. I encountered that problem once with Cakewalk Music Creator 2002, and the problem was that I'd accidentally assigned the same MIDI channel to both tracks. That's obviously not it in your case. Are you using General MIDI? If your using that, I haven't the slightest idea. If your using Garritan Personal Orchestra, by any wild chance, (since that's what I use most of the time) did you make sure that in the GPO window you have each patch set to the correct channel? Make sure you don't have both flute and bass set to MIDI OMNI. That may cause a problem.
FYI: All I've been writing is random thoughts. I can't sleep tonight, so for all I know at the moment, none of this could have made any sence at all. Good luck with fixing your "error". I'm sure you've already tried this, but a good reboot can't do any harm.