What do you suggest? To move the applications every time the taskbar is shown?
Also, have you considered disabling taskbar transparency?

Currently, you can do this with Taskbar Inspector: double click on the AppID, right click and choose to close the windows. Not super-quick, but as the action is not very frequent, I think that it's good enough.

Heh. I changed it to "The 7+ Taskbar Tweaker Team", before someone else starts wondering about my personal habits :)

A duplicate of:
http://tweaker.userecho.com/topic/604551-first-use-of-show-desktop-after-launch-7-taskbar-tweaker-with-enabled-disable_topmost-removes/

Thanks, but I'm not able to download the file. What I see is a page which is mostly blank.
Could you upload it to a different place, or email it to me?

Should be fixed in v4.5.8.3 beta.

Sounds similar to this issue:
https://tweaker.userecho.com/topic/270602-thumbnails-not-displaying/
Is that it?