Sounds like you have the mechanics right and the files in the right place. Since it used to work and now it doesn't the question is "what changed"?
First guess is privileges but it really could be anything. This is the point in time where you want to seriously re-evaluate the whole deployment to make sure it is up to all the best practices. Because something changed that affected FMS and that should not happen.
Can't help you beyond this unfortunately; this is the kind of thing that requires access to all the log files and the machine itself to scrutinize it.
And information on the platform (Mac OS/Windows), which version of the OS and which version of Filemaker Server.
With this information there may be someone here who can advise you.
If it is Mac the setting of the permission for the folders can be crucial.