I hadn't really configured anything until now, but I wanted more plants per chunk (which it is ridiculous that this even exists anyway). I open up the config file, and change the value and hit save. I restart the server SEVERAL TIMES, and the value isn't changed. I still cannot plant any more plants.
Edit: THIS APPLIES FOR ALL CONFIGURATION, INCLUDING BUT NOT LIMITED TO OP STATUS, WHITELIST, ALL MOD CONFIGURATION ETC.