Are you getting this for every hand? Please enable logging, reproduce the problem by playing a few hands on a single table and submit your PokerTracker.log and PokerTrackerHUD.log files (zip/compress them first, call it logs.zip) to the Support system , and link to this thread in the reference field of the ticket so that we can investigate.
After you finish importing a session, close down FT and check for any old hand history files - if there are any, move them manually to the 'processed' folder.