Heather McCue posted a possible solution to the problem of file corruption when using the OS X version of Filemaker Server. Basically it was a timing issue, were closing the database or stopping the service does not immediately release the files, although it might appear that way to the user. Waiting for several minutes before doing anything with the files seemed to solve the problem.

I have run into problems of corruption occurring after closing the file by selecting stop serving on the config program on OS X with no users logged on for 4 hours.