Here is a weird one, that I think is related to the Apple TV downloading from iTunes in the background while running XBMC (have not seen it do this before, and this was the only thing happening different, so that is what I think caused it, but I kind of hope that someone else can shed some light if they have seen / not seen this issue in similar circumstance...).
I asked the AppleTV to buy some Mythbusters epsisodes (hey, only 99c), then hopped into XBMC and was playing a show (standard xvid avi).
Anyway, show played fine, but when it finished, the remote would not navigate XBMC and I could hear the standard Apple TV 'bloop' sounds when I used the remote (I have sounds for remote turned off in XBMC, so I know it wasn't this).
Restarted the ATV, and back into XBMC and start another show - same thing.
Now I have been playing and using this for a few weeks now and not seen this behavior, the only difference being that the ATV was downloading shows in the background.
When the ATV has enough of the show downloaded, it pops up and asks you to press Play to watch now or Menu to watch later.
This question of course does not show when you are using XBMC, but I wonder if it is losing focus, and frontrow is taking over the remote again when it does this in the background....