Just in case anyone else is in the same position as myself here is what PT Support said....
Thank you for contacting PokerTracker Support. The new Full Tilt poker
client released today is not currently supported by PokerTracker 3 due to changes in the hand histories and seating options. Hands that do not see a flop will work, but any hands that reach postflop will require a software update. At this time all of our development resources are focused on PokerTracker 4, if you ae a Windows user we advise you to upgrade as soon as possible to take advantage of the 70% or greater discount when upgrading, PokerTracker 4 will support Full Tilt's changes later today when the new update is released.
We no longer develop new features, changes, or additions to PokerTracker 3. We only fix bugs at this stage, and we will continue to fix bugs for some time though. Changes in FTPs hand histories are not considered a bug... since we predict that the OS X version of PokerTracker 4 will not be available until the end of the year, we have decided to release updated Full Tilt support in PokerTracker 3 in our next PT3 release as a way of helping those of you who are waiting for PokerTracker 4 for Mac OS X. Unfortunately PokerTracker's next release will not be available for another 2-3 weeks"