I can't tell for sure but it could be your sequencer. Have you tried just playing a midi track from the sequencer, or saving a midi file then playing with a normal media player? What i'd try is to play using midiox instead of your sequencer, just to rule out any suquencer problem. Midiox is an application that just passes midi messages betweet midi sources/destinations (it can do transforms, filtering etc but it should not concern you for this test). Supposedly midiox has tight timing so if it still fails, then there's something to how the hardware is configured. Good luck.
http://www.midiox.com/