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In Windows there's the option to assign a key combination in the properties of every shortcut (see screenshots). When these shortcuts are placed on the Desktop or in the Start menu, they act as global system hotkeys that can be used to launch a document or activate a running instance of an application.

The problem is that these hotkeys occasionally stop working on my Windows 7 x64 system. They simply have no effect when pressed. I can verify that the keys are set using the free Windows Hotkey Explorer (although I'm not sure whether it checks the system hotkeys table or it simply scans the .LNK files). It's also not an issue of the Ctrl, Alt, and Shift keys getting stuck (either physically or programmatically).

The problem always disappears after a while, which is both fortunate and frustrating. I haven't been able to figure out if that's due to a conflicting application being closed, minimized, or losing focus, etc.

Does anyone know what's causing this and if there's a way to fix it?

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As explained in The Old New Thing, this is a bug caused by a Windows feature. The shortcuts are supposed to be temporarily ignored when an application is in fullscreen mode, but sometimes they get stuck in the suppressed state. Pressing a system hotkey involving the Windows key (Win+E, Win+B, etc.) gets them unstuck.

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