So, I've got a project that I am trying to render out as audio, but there is one track that is giving me trouble. It is an instance of a VST synth with a lot of pitch modulation automated. In the project it is perfectly in time during playback, but as soon as I try to freeze or bounce it, the timing goes off in some sections of the automation. Any suggestions?

So, apparently if I choose to solo the track, bounce it as a mix with track solo on, it comes out correctly. But if I freeze the track or try to just bounce the one track, the timing goes off. Doesn't make sense, but at least it is a work around.

Yep - I've had similar issues with automation timing when recording a mixdown track back into X2. Normal playback without recording is OK.

Try just freezing the synth not the track

Also use the SLOW bounce feature not the fast bounce. Bounce puts it in a new track as audio. Slow bounce lets it take it's time processing. 

Then simply archive the old synth/source track so it's not being processed in playback..... I think freezing and muting the synth track is the quick way to archive it and take it out of the processing loop. Since you have a good audio slow bounce..... mute the synth/source since you don't need or care what the fast freeze/bounce sounds like.