I opened a project and was surprised at how wimpy the toms sounded. I had used Slate Trigger on them and I tend to freeze tracks when I put plugins on them to save CPU. 
 
I unfroze the toms tracks and I could then hear them properly in the mix. Then later in the track there was a guitar solo which was completely missing. I unfroze it and it "reappeared".
 
What these tracks seem to have in common is automated mutes. I refroze them and they were fine.
 
Is there an explanation for this?

Freezing will not embed automation, nor will editing a frozen track. You need to bounce down the track using "Bounce to tracks". Freezing a track is meant for saving resources not for editing.

Thanks for the clarification, Chuckebaby.

So is there a rule of thumb when working with vsti's?
 
For example.
Freeze while tracking.
Bounce when mixing/mastering.