I don't know if it's a bug in Evernote or Windows - but not a feature for sure. The same symptom occured in Photoshop when clicking on any element of Tools bar - and it was a Adobe PS bug. It might be the case with Evernote, too, perhaps. Maybe it happens only when using Wacom pen-like tools instead of a mouse or touchpad. Anyway I would be happy to find a solution.
Usually it goes like this (Oh, as it happened in this very moment!)
- There are tags and notes among my Shortcuts at the top of the left panel.
- I simply clicked on one of them with my Wacom Intuos pen (that's like a left click with the mouse)
- That choosen shortcut suddenly disappeared from the Shortcut menu (it is still there among tags, 'cos it's a tag)
- So I have to right click on it - under tags - and choose 'Add to Shortcuts' in the pop-up menu
That's all. Mysterious.