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Alt1 has been (randomly) changing windows to be Always on Top, only repairable by closing and reopening the window that this affects.
So far I've had this happen on three occasions, (once on chrome, twice on the RuneScape client) and now leave Alt1 closed absolutely as much as is possible.
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Alt1 only changes topmost state of other windows in specific situations.
There is an option to enable a hotkey that does this (by default it's off)
Toggling the various buttons on the alt+3 feature can change topmost state, you could use this to revert the topmost state if it happens for whatever reason
Messing with the topmost state of alt1 apps using a different program than alt1 could theoretically cause this.
It is hard to say what caused this for you since i've never heard of this problem before. If you can provide any extra information it would be helpful. In the meantime the easiest way to revert the topmost state without closing the program would be by selecting the affected window and pressing alt+3, there is a checkbox there to toggle topmost state of the active window.
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