PokerStars had an update today that added some new lines of text to the hand histories which PT could not handle, "Uncalled bet...".
Here is the patch
http://www.pokertracker.com/products/PT ... 21702a.exe
Mike will have the PTO/S patches up later today.
To get the hands that were missed because of previous errors you'll have to reimport the hand history files.
If PT has already moved the files to your processed hand history folder then you will have to move the files back to the PokerStars hand history folder and then use the Force Import button on the PokerStars auto-import window to reprocess the files again and pickup the hands that gave errors the first time.
SINCE PT3 IS SO CLOSE TO RELEASE DATE you can also consider using that now in preparation for release on May 15...
http://www.pokertracker.com/products/PT3/