Keynote and Apple Aluminum Remote

I have used Keynote for a long time now and never had problems using it with a remote control.

I updated to Mountain Lion recently and **** broke loose! I cannot get Keynote to work with a remote if I am showing my presentation on a secondary display (an LCD TV connected to my Macbook Pro via an HDMI cable). I did manage to reset the SMC (System Management Controller) but it solved my problem only temporarily. I know the problem is not with the remote because when I use it with Keynote and I am not using a secondary display, it works perfectly. BTW, iPhone and iPod touch remotes are not enabled.

Anyone knows how to solve this?

TIA