Using terminal commands, I was able to get it working correctly. I had a server that did this.
Check out the commands "quota" "quotacheck" and "setquota".
I did a setquota 200000 (I know this isn't how this command works, yet when I do it, it works).
After that, run quotacheck for all your volumes. I run it verbosely.
Then check a user's quota to see if the limit is there. Below are the commands I typed in:
At Terminal:
setquota 20000 <enter>
quotacheck -av <enter>
quota <user> <enter>
Remember, that you must either use the "sudo" command or be root to run these commands. After this, my quotas worked correctly.