I can't diagnose your problem but there are numerous threads advising to never let Time Machine touch the FileMaker Server folder. I won't let Time Machine touch files currently in use on a local machine either.
Thank you for your response Rick.
I knew I was in trouble when the TM restore did not act as expected. Fortunately FMPro is still keeping the current data in a safe location ... somewhere. The backups are fine and files are still accessible. If I only knew where they reside.