Depending on the software you are using my answer may or not apply. I use Cakewalk 6.01 with a STUDI/O card and an ESS Audiodrive just for the midi part. This problem happens when the audio and midi cards are not syncing well. In Cake, selecting "use wave out for timing" cures the problem because the program uses the audio material as a sync source. It should also work with the MOTU problem so try it, if you use Cake.