This shouldn't happen again after beta 25. You're not uninstalling or deleting any files, are you?
Is it keeping your HUD config but losing the positioning information?
I don't think a log file would necessarily help, but a before-and-after of your layout files would be good.
Do you have a backup of the layouts.pt3 file from before you installed the upgrade? Have a look in C:\Program Files\pokertracker 3\data\ and see if there is a layouts.pt3.backup file dated from the time you ran the installer.
If so, zip that and the new layouts.pt3 file (select both, right click > Send to Compressed Folder) and attach the .zip file to a
Support ticket.
Please note a site and table type/size where you play and had your HUD stats positioned how you like them.