Thank you for the post.
A few more questions to assist us in narrowing this down:
1. What is the operating system of the FileMaker Server?
2. Were the files re-uploaded using the FileMaker Server Admin Console?
If the FileMaker Server is running Mac OS X, then possibly the files were copied into the server's directory and did not receive read/write permission for the fmserver user. Close the files and remove the files from the server. Afterwards, upload again using the FileMaker Server Admin Console.
Uploading the files in this way allows our software to properly set the permissions. Please let me know if I have misdiagnosed the issue or if you have any questions about the troubleshooting outlined above.
Hmm. In my very limited experience the best way to get the files to Server is to use FMPro 13 command to upload files to the server. Interestingly enough, once I've done this one time I can freely use Mac OS to drag files from the server or add the same files to the proper Server folder at will. All permissions change properly as the files are moved from one location to another.