What do you mean by "non-Filemaker activity on CPU"? You don't descirbe any Non-FilMaker activity here, just closing the files.
Do you have backup copies of these files?
If you perform a recover operation on these back up copies are any issues reported by the recover?
This is a test to see if the files may already be damaged before ever closing the files and FileMaker.
Have you run any diagniostics such as checkDsk on your computer? That can rule out issues with your hard drive that may be damaging your file when it is saved back to disk when you close the file.
By that I meant something outside the application. I had this happen many years ago and traced it to a Service Pack issue; now I suspect it has something to do with antivirus software trying to scan an open FMP file and corrupting it in the process. Crazy things like sending a message about an "invalid relationship" when all I am trying to do is delete a record. Article in the FMP Knowledge Base, plus a call to live tech support, led me to Answer ID 4807 which indicates the FMP files can be corrupted by antivirus software if a scan is run on the file while open.
Why this continues to be a problem since FM version 7 boggles my mind, quite frankly. Why hasn't Filemaker fixed this over the last FIVE versions??
Correct that: Answer 5807.
So, I have blocked my DB folder from the antivirus scan (which seems risky but whatever). Have been using FileMaker since version 3 and so stunned that the company has let this issue continue for so long.