Your comments

Oh wow, thanks so much! It works perfectly now as far as I can tell.
It's really impressive how you keep up with all of this.
I'm using Windows 8.1 64-bit, and Taskbar Tweaker v4.4.6.2 beta, though it was present in the non-beta version I had as well.
Here's my options layout: General and Advanced
And Taskbar settings: Here

To cause the bug to happen, I just
1. open two instances of the same program (they will combine on the task bar)
2. Click on them to bring up the thumbnail selector thing
3. Hover over each thumbnail and mouse wheel down to minimize it
This causes the thumbnail selector to get stuck open.

I should note as of today I finally ran my Windows Update, which broke the Taskbar Tweaker (pretty sure it's the Windows 8.1 update 1 thing), so I'll probably have to do a system restore to provide you with more info if you can't reproduce the problem.

Hope this helps! I really like the program even after only using it a couple days! I'll probably end up donating to the alpha Windows 8.1 update 1 endeavor :3