This was discussed in the blog comments:

http://rammichael.com/7-taskbar-tweaker/comment-page-13#comment-2569

Quoting myself:

"In fact, I’ve encountered this issue, but it happens so rarely (happened to me once or twice, literally) that it doesn’t really bother me.

I can’t do much with it as I can’t reproduce it.
Also, I’m not sure it’s the tweaker’s fault. If it happens often for you, you can experiment and see whether it happens without the tweaker running, or with it running with all options off."

You can't do that.

What you can do is group these icons together so they take less space: select them in taskbar inspector, right click and choose Change Application ID -> random_group_x.

The bug was already fixed ;)

http://rammichael.com/7-taskbar-tweaker-v4-1/comment-page-1#comment-2641

The issue was introduced in v4.1.7, and was fixed in v4.1.8.

Sorry for the inconvenience.

Hi Adam,

I use this option quite often on my PC (Windows 8 64-bit), and it works every time. One exception is when the active window belongs to an elevated process, like regedit.

I can't do much without a way to reproduce it. Try to notice what window is focused when the issue appears. Other than this, maybe one of your other applications conflicts with the tweaker.