is this your problem, here's the solution
Ok I thought I would post this as I have just sorted out my problem with PT3 today. If you have played over 200 hands then you need to email Stars support and ask them for the x amount of hands you need over whatever time period you played. I played around 800 hands and they emailed the hand history over to me within 30 mins. They send it to you in notepad form , I just put the file on the desktop.
Next you need to install the very latest version 3.11.9 BETA from here
https://www.pokertracker.com/products/PT3/download.php which fixes the every hand at showdown loses problem.
Next you need to purge your sessions which had the data from today which was incorrect by going Database - Database Management - Purge. It will then bring up every session you have played. Then select the sessions you want to purge from today, this will take them off your database, you can hold down ctrl key and click the mouse to select more than one session.
So now you don't have the hands from today showing in your database. Next step is to go Import - Manual Import - Import From File(s) and then select the file from your desktop that Stars sent you and hey presto, problem solved.
I hope this helps others who have had the same problems.