FINAL UPDATE
It appears that PokerStars has now resolved the issue. If you are experiencing problems on PokerStars, please make sure that you download and install the latest beta version linked below.
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PokerStars made an internal change to their hand histories in the past few hours and by doing this introduced a bug where the hand history is listing the winning player and amount as losing the hand therefore PokerTracker is going to import these "winning" hands as losses (how they are defined in the buggy hand history).
PokerStars is aware of this problem and are working to get a fix out as soon as possible. In the mean time, please make sure that you are using the latest beta version, linked below so that you are ready for when PokerStars fixes the bug they introduced in their hand histories:
UPDATE
PokerStars still has not fixed their hand history bug therefore we got tired of waiting and released 3.11.9 BETA which should work around the problem. Please download and install this latest version.
PokerTracker v3.11.9 BETA - Download
PT4 users -- we'll try to get a patch out within 24 hours if PokerStars does not have the problem fixed by then.
Best regards,
Derek