Having the same issues here too!
We have found a work around though with an application called Remote Buddy, currently on a free trial.
The solution we have come up with is to go into the settings on Remote buddy and configure it to work from here. Go to preferences and select Keynote from the list on the left - Mapping from the tabs at the top. You'll see the play/pause bit there. To map this to pause video you need to create a custom action and then in the Keystroke box towards the bottom put in the letter 'k'. Keynote's keyboard shortcut to pausing videos. Once you have done this then you are good to go.
We were hugely disappointed also by the lack of information and help when trying to resolve this situation, both in store and over the phone. Does anybody know if this is even being looked at by Apple/Keynote, or could be solved in a later update?