How do I give permissions for the nether to my users?
Solution 1:
There is the sub-group "worlds:". This most likely governs what the group can do in said world. Try typing the name of the nether file (by default it is world_nether) in the format shown with "creative". Then add the node "permission.build: true" along with anything you would allow them to do in the nether.
Sorry if this does not work as I used a different permissions plugin in my limited server hosting days.
Solution 2:
I believe there is a separate config file for the Nether. I had this problem on a server I administrated, and we had to copy the World config into the Nether config for it to work. This was, however, on a Multicraft server, so it's possible that it had changed the layout.