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I don't know much about sequencers. But maybe a concept from the "raw audio" world would help. Riven's comment in this thread is what is most pertinent:
How are MIDI sounds launched? Are you doing them singly? Or can they be placed in the context of a running sequence, running timeline? If the latter can be done, then you have a better chance of accuracy.
There's also a link, in that thread, to a good article about timing issues for audio, in my first post there.
It might be helpful to enqueue the MIDI events as they arrive, with a timestamp, and use the timestamps when calculating when to feed them to the Sequencer. But as I said, I could be way off, as I haven't worked with MIDI in Java yet, and don't know if that even fits the model of how things are done.
But it's not like you've gotten a lot of help here from anyone else, yet...
You might try StackOverflow forums.