After a lot of forum research and experimentation, I have found a set of parameters that seems to work well on Pro Tools 9.0.6 running on my iMac i7:
Enable Midi Clock in PT
Set Virus to receive Midi Clock from PT
Make sure there is a 1-2 bar preroll for recording, playback, overdubs.
Set all Virus instrument tracks to a Midi offset of -2259 (Event-Midi Offset)
Set Delay Comp to Long
I have set up an 8 bar loop as a test and have six tracks running (5 Virus, one Drum track with Strike) in perfect sync. They also stay in sync when I loop the track. Three of them have an Arp enabled.
-dj