I'm not certain the sync problems are the fault of the Virus.
This "drunk" effect can happen whenever you are sending MIDI time clock through multiple machines.
In the past I've used all manner of groove boxes & drum machines as the master. Whenever I've had this problem I've always found the best solution is to have everything synced to the sequencer time clock, in your case Ableton. Also try not to have too many things lined up in series as the further down the chain you get the more noticeable the effect can be.
Isaacanthony you said yourself when you use the MPC & loop a 4/4 kick they almost stay in sync, you should be able to set things up so they stay absolutely bang on sync with each other. Try different MIDI configurations & see if that helps, is it possible to have the MPC connect to Ableton then Ableton connect to the virus?