If you are ever trying to troubleshoot a system script that will be run by the fmserver user on OS X you can do the following to replicate what the server is doing with terminal.
1. Type su
2. Enter the root user password
3. Type su fmserver
4. Type whoami and it should return fmserver. This last step verifies that you are in fact the fmserver user.
This is what it should look like in terminal:
servername:~ currentuser$ su
sh-3.2# su fmserver
An example of what you can do at this point is execute a shell script as fmserver.
sh /Library/FileMaker\ Server/Data/Scripts/example.sh