I'm having a similar issue! My custom shortcuts randomly (pattern not known) stop working until reboot. The underlying commands still work, the keyboard still works, but no custom shortcuts will work anymore, no matter how simple I make them. Also, when this happens I can no longer assign CTRL+ALT in the same combination. I can assign CTRL+J, or ALT+J, but not the original CTRL+ALT+J, but I can assign CTRL+SUPER+J, it just won't work after assigned rendering such workaround useless. Weird. Other keyboard shortcuts work, though I don't know if I have customized them previously: navigate to workspace number # = CTRL+ALT+#, still works. It's a minor issue, but annoying. Also, maybe important, my setup makes CAPSLOCK behave like control and that's what I use for CONTROL, though all the above still applies when I try using the actual CTRL key, too.