I asked this in the PT forums and here are the results:

Answer: Go to the Game Notes tab and click the "Select All" button. Now, sort the top data section by rake so the highest appears at the top. Do you have any that are greater than $3? If so, you may have loaded these hands using an older version of PT - Party changed their hand history format a while back and was causing some high and even some negative rake amounts, this could explain the problem.

ME: YES, biggest rake was $293 in a $333 pot!! I have now downloaded the patch but is there any way to fix this problem to see the real stats?
EDIT: Do you know if there is anything else wrong with the stats PT has given me besides the rake?

Answer: You need to delete an reimport the hands. On the Game Notes tab, click the Export button to export all these hands to text files. Then use the Utilities/Database Maintenance and Options window to purge all these sessions and then use the File/Import Hand Histories/Tournament Summaries - Select Files To Import button to import the files you exported in the first step.