Here is what I did to fix it !
OpenDirectory has to be setup with its own utility from Admin Server utilities. So I removed the main server from the Network Account server under Account of System Preferences. Then I clicked the button to configure OpenDirectory server under OpenDirectory section of Admin Server utility. I chose to configure the MacMini server as a replica, works like a charm !
FileMaker server now reads the user list from the OpenDirectory of the MacMini.