Yes, that's a known and documented limitation.
Doing a proper implementation with jump list support will be much more difficult, and I don't plan to look at it for now.

There's not much I can do with the provided details.
If that's still relevant, please either provide a way to reproduce the issue, or try to find out which option of the tweaker, if any, causes it.
A video which demonstrates the bug might also help.

Should be back to normal in the latest beta version.

Should be fixed in v4.5.10.2 beta. Please try it.
I'm closing it as a duplicate of:
http://tweaker.userecho.com/topic/314270-icon-of-closed-window-blocking-active-window-to-take-its-spot-in-the-taskbar/

Should be fixed in v4.5.10.2 beta. Please try it.

Please try the latest beta version.

Looks like a duplicate of:
http://tweaker.userecho.com/topic/314270-icon-of-closed-window-blocking-active-window-to-take-its-spot-in-the-taskbar/

Closed due to a lack of feedback. If still relevant, please provide more information.

Since v4.5.5, you can use the Mouse Button Control advanced options to minimize/close all items of a button group.

If that's still an issue, please provide more details. Closing for now.