I would suspect the midi file first, since any time I've had this problem, that's what it turns out to be. Take a look at the midi file in piano roll view. If you see several extra long notes, with overlapping notes (the same note being keyed before the end of the last time it was keyed), that's probably it.

There is an update for the SD-2, just in case you're not running the latest version. http://www.ketronus.com/downloads.php

While you're there, you can pick up some drum loops for it as well, if you haven't already.

Hope this helps.

Later,
Jim