I ran into similar problems exporting a mix while using VSTi synths. I found that if I unchecked the "Fast Bounce" option, most of the time it fixes the issue. For the times that it doesn't, enabling "Audible bounce" in addition fixes the issue completely.
The issues included:
- time-based effects (echo, tempo-tracking lfos, etc) not tracking the project tempo when they should.
- Unsmooth/jumpy changes (Pitch bends, portamento, etc).
- mis-timed notes.
Note that changing the midi buffers does not fix these issues. Its one or two soft synths out of a bunch that gets this issue. Even if there are multiple instances of the same synth in the project, one of them may get the issue while the other does not. If I start the project over from scratch, I may or may not end up with the issue.