I currently have application hooks disabled as I was getting stutters in games due to it. However, I've noticed that occasionally when you have an application with multiple windows ( for instance firefox with two separate windows ), selecting a window from the secondary taskbar will only pull up one of these windows and clicking the other will not do anything and can only be selected from the primary taskbar.

Edit: After restarting, it seems to be functioning normally again so I'm not quite sure what caused it. I've seen this happen a few times though. I'll try to see if I can get more info if it happens again.

Haven't seen any further issues with this so I'm guessing something happened that caused it to break and its unrelated to application hooks.