The piece--all MIDI tracks, no audio. The two tracks in question were formerly playing through a GM softsynth, and played back fine. I changed one to play back through a GPO solo violin, and it still played back fine, still in sync with the second track. But when I changed the second one to also play back through GPO, a solo clarinet voice (same instance of GPO, different MIDI channel), the two voices were out of sync!
What could cause this? Differences in latency between the voices? If so, that's a bug in GPO, because the different instruments should be able to play in sync with one another.