Haven't touched protools in about 8 years but the little I did use it made me loathe protools. So, on your MIDI/Instrument tracks, they are off sync with each other during live playback but when you bounce them they are synced up without any adjustments by yourself? That's pretty weird if that's the case ... so no advice on that one other than what you are already doing.
It was happening during playback though I didn't bounce so I'm not sure if it was in sync when bounced, I think it would continue to be out of time. It was only one effects plugin (mondo mod) that made it go out of time and I have managed to achieve the same effect without using it so it's not a huge issue. I just wondered if anyone else did this technique.
I have heard that pro tools isn't the best for composition, but it's the DAW I've used for 5 years or so. I have bought fruity loops fairly recently and that seems pretty cool. But I like a lot of the functionality in pro tools.