yeah, RMXP just uses different instruments that a MIDI player like 2k3, and sometimes doesn't use an instrument at all. Some songs actually sound better to me, like Repeating Battle from 2k...3? might be 2k, but still...others may just be a beat drum cause all the instruments are being ignored...
u know, rather than converting or anything like that, u should probably use Audacity's record while playing the song to "re-record it." This'll make sure your new track has 100% of its original quality, and then u can just export as MP3.
pm if u have troubles or ?'s about audacity.