I installed the 4.07.1 mac version on my iMac and i still get the issues with the permissions.
After looking at the pokertracker 4.log file myself i noticed that macosx wasnt able to create a directory (Users/Shared/Library/Preferences) it seems that it needs that directory because after i create the Preferences folder manually it worked perfectly.
Hopefully it can help other people which are still struggling with the issue themselves after the new mac update