Going to go ahead and bump, no one has any ideas what might be causing this?
I don't think your problem statement is clear enough.
What version of FMS?
Is this a server-side schedule?
Do you have FMS configured to NOT run as the default account (fmserver on OSX, 'local system' on Windows)?
FMS by default has access to its own documents folder so it is not clear to me why you need to change its privileges.
OS: El Capitan
FMS Version: 15
Is this a server side schedule: Yes
The filemaker server user is not the default account
Through some trial and error I've found that without the user added to the folders permissions, the export and import scripts fail. The problem is that regardless how many times I add the filemaker user to permissions, it will get automatically removed after a short period of time.
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You should never have to touch folder permissions in the FMS folders for FMS to have access. It is all set up during installation. If you are manually adding the FMS account to the folders then there is something wrong with the installation.
I suggest uninstalling FMS, delete all FMS files and folders except your Databases (move them somewhere else), reinstall FMS, move your databases into the new FMS Databases folder. On Mac Only propagate the Databases folder permissions to all the FMP DB files in the Databases folder.
This is the scenario I was hoping to avoid but, If there's no other way around it, it's probably my only option.