Ahh. I think I had that happen to me once on a different game, but it only really triggered the one error message before crashing. I fixed it by running the affected mp3 through Audacity and making the bitrate constant instead of variable (i.e.- re-exporting it). If I knew which filename the song that's meant to play was I'd give fixing it a shot on my end (or just go through all of the mp3s one by one).
I don't know if RM2003's incompatibility with variable bitrate files has anything to do with codecs, though, or why it only seems to happen to some people when they extract RM2003 games.