You may have to just completely reset the config files for Essentials and start over again, I don't know of anyone else with this problem, I would highly suggest to just reset your server and go over again and change everything as you go, BUT if you cannot, then try to:
remove essentials > stop server > go to the files and delete all the essentials folders and config files > start server, then stop it > install Essentials Plugin and Vault > restart server and then go into the file manager again and then edit the config files and then after your done make sure to save it and then stop and restart your server,
But before you do anything with that, Make Sure that you have Vault installed because essentials won't work, I would try to reinstall Vault before doing the Essentials mess!