I've had a similar problem with 'looping points' when using instances of NI's Maschine in VEP and piped through /slaved to Ableton Live.
If I have, say a 16 bar loop set in Live every time it reaches the beginning of a new loop the audio glitches for that first beat from the Maschines in VEP.
The only solution I've found is to set the VEP Plug-in instance latency set to 'None', which raises the CPU level in Ableton to about the same as if the Maschine instances were in Live (which defeats the point of using VSP really).
Is there possibly some sort of tempo/loop/sync issue here?
(Maschine's play nicely when directly inside Ableton Live)
Cheers,
Alan