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This is a note for such like me, who meet this problem. This in my case was connected with different keyboard layouts.
Some my custom defined keyboard shortcuts stopped working, but some are still working. I speak of Keyboard shortcuts, not Window Manager shortcuts.
I.e. my Alt+F1 to opens Application Menu - works
winkey+e (<Super>e) runs thunar - doesn't work
Finally I found out that it's connected to the order of keyboard layouts.
I have Ukrainian and Russian keyboard layouts installed and here ua was at the first position (now moved it lower):
So I found out that <Super>e doesn't work, but works like <Super>Cyrillic_u(switched to Ukrainian keyboard layout) if ua layout is the first.
So I deleted the ua and ru keyboard layouts and added them again to make the us layout to be the first.
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