I think it's a privilege problem, not anything that's caused by HotkeyNet. Somehow or other, your main WoW is getting launched with a different set of account credentials than HotkeyNet or the other WoWs. I think this is why Windows displays "User Administrator." This sounds like "run as administrator" but they are two different things.

Before I go on, you may not need to fix the problem. If the main WoW is always in the foreground, you can add "PassThrough" to all your hotkeys and everything will probably work even though the problem isnt' really fixed.

If the main WoW isn't in the foreground, then you'll need to really fix the problem. I suggest looking at the way in which that copy of WoW is getting launched.

Edit: Oops, our posts crossed. Grats on figuring it out.