I confirmed it with a test. The problematic patch is on part 11. If I mute part 11 and move the patch to part 14 the note won't play at all (out of DSP- and I confirmed my MIDI and output settings were correct, too... you can hear the patch if you play it by itself). If I mute part 14 and un-mute part 11, I can hear the note again- but of course still with the pop.
So, I learned something about the Virus, but it didn't help me with this issue.
However, I just went through all the patches currently loaded and set any instruments that were only playing one note at a time in the song to "Mono 1", and this appears to have given me enough juice to avoid that pop.
I am still frequently hearing an unwanted click later on (around when this FX patch stops playing), but haven't diagnosed it yet. It is quiet enough that it might be acceptable for my purposes, though.