Elementree, I have a question, do you have protools on mac or pc? I recently moved to mac but i had protools digi 001 since 5.x and subsequently over that time moved up to 6.4 running on pc and xp for the last 7 years, I found a big difference once i upgraded to the 003, 7.4 and Mac the most annoying thing that i dealt with was timing, and getting tracks dumped, the problem i had was no matter what settings or compensation by pre roll etc, a small portion of my wave would be cut off hence making a perfect loop virtually impossible forcing me to dump each track fully instead of just dumping 8 or 16 bars, looping and editing in audio, I thought it was a sync problem or something with the mpc or one of my other pieces of gear in the midi bus, but when i upgraded to the mac and the new set up all of these problems went away, I am thinking that either there was some issue with my hardware platform or configuration that introduced the small sync offset, also when I tried punching it would also be off so this might be something to look at.
I also found the below information off of the digidesign website also, it just mentions some sync problems that might introduce issues in a session also, especially if you are tracking beats with midi and protools, which is how i dump.
MIDI sequencer is slightly ahead of Pro Tools when controlled by MIDI Beat Clock from Pro Tools.
Some older pieces of gear (particularly Roland gear) interpretted the MIDI spec differently. They treated the CONTINUE message as the first F8 beat clock i.e. they start clocking ahead immediately after receiving the CONTINUE message. This results in the external sequencer being 40 ticks ahead of Pro Tools when played back from anywhere other than the session start.
Since Pro Tools currently doesn't allow you to specify a "MIDI Beat Clock Offset", the only workaround is to always start playback from the beginning of your session. This is not a bug in Pro Tools, but may be addressed in a future release of Pro Tools.