I have the unfortunate occasional habit of resting a finger on the shift key while I’m thinking. Up comes the Filter Key popup. No matter how I exit it, I’m stuck with a screwed up shift key and have to reboot.
My wife just ran into this issue when she was playing World of Warcraft (which often requires multiple rapid keystrokes).
We resolved it by doing as everyone else has suggested (Control Panel>>Accessibility>>Keyboard), but in addition to unchecking all the boxes on that tab, click on the “Settings” button next to each option (filter keys, sticky keys, toggle keys) and on each, uncheck the “Use Shortcut” box. This should do the trick.
ETA: I have no idea why the shortcut still works when one has already deselected the option to use each “feature” - .