I am not aware of any specific issue that would cause that but if this is on PokerStars and you are using the cashout function then you should use the 'My Currency Won (Including Payouts)' statistic instead. Also if you play on more than one site make sure you have aliased your screennames:
Guide: Player Name AliasesIf you want to follow up on this please send all relevant information about why you believe this to be the case to us in a
Support Ticket along with the sample of hands provided to you by your poker site(s). By default PokerTracker 4 moves your files to your 'Processed' folder:
\Users\{Mac Login}\Documents\PokerTracker\Processed
Guide: Processed Files