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Sorry for the late reply. Could you please email me, so we could do the testing without polluting the comments here?
My email address can be found here:
http://rammichael.com/about
Thanks.

I could reproduce it. While this indeed looks a bit wrong, I'm not sure that it has a straightforward fix.
In general, if you want your window to not get minimized, you make it topmost, with is the exact opposite of what disable_topmost does.
See also: https://devblogs.microsoft.com/oldnewthing/20040527-00/?p=39153

The registry setting is quite standard, I see no reason for it not to work. Could you check whether it's listed in the msconfig startup section? In the autoruns utility? Also, did you notice this problem with other programs?
While the tweaker doesn't provide such a feature, you can use a registry tweak to set a maximum number of displayed thumbnails. If the amount of thumbnails becomes larger than the specified limit, a list will be displayed instead.
More details:
http://www.sevenforums.com/tutorials/75804-taskbar-list-thumbnail-previews-mode-change.html
There was a hardware failure on the server. The website is restored now.
The database backup is from the 29th of January. Unfortunately, there's no newer backup.
I might consider it for one of the future versions. Please create a new post about it.