Some hotkeys randomly stop working

I have 4 spaces with hotkeys assigned (ctrl-option-cmd 1/2/3/4). At random time, hotkeys for spaces 2 & 3 just stop working. 1 and 4 seems to still work. Closing TS and reopening seems to solve the issue, but its happened twice this morning.

I have added a second display quite recently. But i just have single space setup on it.

Any ideas?

I am having the same issue along with hot corner settings not working. When I move my mouse to a corner, the screen flickers but nothing occurs. I get the same result on all spaces. I am running Mavericks