Strange MIDI Timing Issues

Just ran into a strange problem using VC. I've got 3 pluck patches programmed that I'm combining in the final mix. 2 of the tracks bounced fine, all the notes are where they should be on the grid. I did have to drag them back a bit ~128th note because they recorded early (it looks like VC is trying to adjust for latency even though I'm not using the Virus USB audio, bleah).
On the third track however the Virus did something really strange. The first note on the track is in time but the second and most of the subsequent notes were almost a 16th early. I said most because one note (just one note) later in the sequence was late relative to the others. This is a track with 2 note chords playing a 4 measure dotted 1/8 note pattern that was copied and pasted, all the sections are exactly the same, nothing fancy
Is the Virus/VC integration trying to be tricky with synchronization? All I want it to do is play what I send it so I can record its audio output.