Ok. We have it working now, right clicking with string on the ground will show the region name. Also, users can use all the commands in the original post. The name of the permissions had changed with meant that it stuffed it up.
Also, where it says areaname it does not mean type areaname it means type in your region name there instead.
So for example if I wanted to put creeper-explosion protection on, and my region was called Miss, I'd type
/rg flag Miss creeper-expolosion deny
Also, you can not change your settings on you [World] region while you're in the nether, end, flatworld, pvp or whatever else, to change the settings on stuff, you need to be in the same world as the land you're changing the settings on is located.