Thank you for the post.
Some questions to assist us with narrowing this down:
1. What is the operating system for the FileMaker Server computer?
2. What process was used to upload the file to the FileMaker Server? Was the client used for uploading or was the file copy/pasted into the host directly?
As Timothy Bentley (Thank you!) mentioned the issue sounds like the host is Mac OS X and the proper permissions were not set because the file was dropped directly in the hosted directory. The first suggestion would be to close and remove the database file, then upload the database with FileMaker Pro 13.
Please keep me updated with any progress.