I and a friend are having this problem as well. We initially thought it was only on a retina MacBook Pro 15, with 10.8.2 and 14.3.1. The arrow keys stop working and so does a Master Cue or other external USB 'clicker' devices as well. This doesn't happen
with Keynote and the machines are all offline during use, so DropBox is greyed-out and not attempting to sync, and it doesn't appear to be any new preferences thing, as that hasn't updated and doesn't affect Keynote. (Also, you can still successfully use the
mouse to click on the on-screen back and next arrows when in presenter view.)
This also happens on several MacBook Airs of various iterations as well. (two flavors of Core i7 and a Core2 Duo)
The funny thing is I noticed it at the same time as I started seeing the transition 'tearing' at the bottom 1/6th or the screen in show mode running to a projector. That seems to be exclusive to the 15" Retina MacBook Pro.
These issues continue to happen after full reboots with PPT as the ONLY app running. I've even done a PMU reset or SMC reset on the machines figuring it was a USB bus issue or something like that.
I wanted to add my 2 cents so I could get subscribed to this topic!
Thanks,
joe