With the change to 1.9 and re-enabling Spigot, I discovered that my old permissions system was no longer usable. I had to switch to a new permission system, and in the course of that messed up permissions for the nether. Fortunately, our new member Tubby_Turtles spotted the issue and let me know, and that issue now appears to be fixed! I also verified that it should work for The End as well. If y’all spot any other problems, please let me know!