Um, is it possible that you have a LST trig condition on one of your midi tracks? If you do, I’d probably check there and see if there’s something that has a last condition applied to it which is causing the midi sequence to cut short on the last pass. Otherwise, I’d say test the Minifreak with something else leading it (another midi sequencer) just for the purposes of establishing which device you need to be troubleshooting.
You could also check in the bug reports topic or the minifreak topic for something similar.