Nice that you found a workaround. Or actually, if the case is that this particular VST doesn't like Fast Bounce/Quick Freeze, it's not even a workaround.
The slightly distracting detail earlier was maybe this:
"...when I exported the audio of the MIDI track and played the file in a different DAW,.."
It maybe gave the impression you thought the DAW was a relevant factor, allthough, when the audio is exported, it plays exactly the same in all reproduction systems. If there are delays or whatever, you hear them exactly the same no matter what software or player.
Your last post makes me think there might be a similar hickup with Quick Freeze as there is with Fast Bounce. Many VSTs don't like Fast Bounce. (I did not know there is a "Quick Freeze" in MC6, you're not talking about "Fast Bounce", are you??)
AFAIK there's no "look-ahead-type" of function regarding the patch changes, so I wouldn't be surprised by minor delays in automated patch changes. Changing of the patch may simply require some time, depending on the patch and synth (loading samples??). When possible, it might be worth trying to position the patch change a little (50-500 ms??) earlier.