Based on the case notes, it seems like there were two issues:
1) You encountered the bug logged in WI 123039
2) You ran into an issue during the upgrade of PIFD as the upgraded DB is in a bad state (missing records in the dbo.AFAnalytisTemplateRule table).
From the last entry in the case, the product specialist asked if it was possible to send us a copy of the DB prior to the upgrade so we can try and upgrade it on our end and see if we can reproduce the issue you encountered. The other alternative would be to investigate the log output of the go.bat script that is used to upgrade the SQL database.
I can see on our FTP that a database backup was uploaded a few minutes ago. I will restore this backup and investigate the issue you encountered as the product specialist working on this case has the day off today.
I'll get back to you via email. Once we've identified the root cause and solution we can come back to this thread to let the other readers know.
In the meantime, if you have any questions let us know!