A while ago I started having a problem in Emacs with setting the mark (Ctrl-Space). It was difficult to pin down exactly what was wrong and I was not able to reproduce it. Just a sporadic thing that sometimes caused the command to be ignored.
Then for some reason I suddenly realised that this was because the shortcut clashes with what Dunst (the notifications daemon) uses system-wide to dismiss the most recent notification.
So whenever a notification was being displayed, my Ctrl-Space would dismiss that instead of setting the mark in Emacs. I just hadn’t noticed the connection.
So the fix was a very simple, just disable the shortcut in dunstrc:
# Close notification. # close = ctrl+space
I can still just dismiss all notification with Ctrl-Shift-Space.