From my own experience, the problem is with Ableton Live (both 8 and 9). I find that the VC plugin completely throws out Live's MIDI clock output. If I sync my Elektron machines to Live's clock then they are a good half-beat late when VC is loaded. I don't have Maschine, but I wouldn't be surprised if it is reacting the same way as my Elektron kit. As soon as I remove VC from the project everything steps back into sync. I think other plugins can mess with Live's timing and latency but none to the degree that VC does.
VC does not cause this behaviour in Logic, even with "Live" mode disengaged. I guess that Logic is managing its MIDI clock output differently, or at least with the correct priority, compared to Live. Much as I enjoy using Ableton for composition, this issue alone is pushing me to learn Logic as my main DAW from now on.