Play/pause/stop on remote stop working

When I first startup Kodi, all buttons on my MCE remote work fine. I have a dual monitor setup though and if I flick over to the other monitor and then go back to kodi the play, pause and stop buttons stop working. All other navigation buttons on the remote still continue to work though. If I restart Kodi it remains broken and only a complete computer reboot seems to fix it. Any ideas what might be causing this?

Thanks