It happened on the home screen and I vaguely recall it happening in Netflix too. It wasn't just a Channels issue, although that's the main app I use. The Apple remote reboot did the trick. I also have been keeping the Apple remotes charged up more...seems like when they get low on juice they'll do strange things.
I felt bad because I was blaming the Function 101 remote for the issue, and their (awesome) customer support even sent a new one, but out of the box it was doing the same thing. That's when I started researching and came upon the Apple remote reboot thing.