The user account that starts the FME Server services must have permission to read and write files in the FME Server installation directory. This user account also requires permission to access any directories or resources required by a workspace.
If you specify any UNC paths or mounted directories in the FME Server installation, the user that starts the FME Server services needs write access to those directories.
If you are not using the Application Server included with FME Server, then the user that is running your Application Server needs the same permissions as the user that starts the FME Server services above.