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Under review
Possible change in the z-order
The z-order/stay-on-top of the other windows (assigned by non-native apps of the Windows OS :P) get changed once a while when you hit the about or help buttons in the setting pannel :(
Customer support service by UserEcho
Is it related to the taskbar or to the tweaker's options? The z-order is not something the tweaker controls, especially not with the main window which is mostly standard. Sounds like the problem is with your system, unless I misunderstood what you mean.