I seem to have fixed the problem with nUI5 by removing all key bindings, and then applying them again. As for nUI6, when I use the key bindings I get the same problem. Spells/Abilities become click-through, and once that happens, and I log out, I lose my cursor and have to open up the task manager and restart WoW :\ As nUI6 is still in Alpha, I'm not complaining
Another problem I noticed with nUI6 is that when I go to the key bindings page, the section for the nUI buttons is missing, and anything I do try to keybind doesn't go through