I've had this problem before many times. The only solution is to power the box off and on, and just like resetting a frozen computer, it fixes the problem.
I don't know how this situation comes up, but I have a theory.
Next time you notice that one of your channels has that message "one moment please etc etc", take a moment and flip through all of your HD channels, I think you will find that 2 or more other channels are also afflicted with this message.
The strange thing is that if you swap tuners, you'll find that those channels are available on the other tuner, but not on the first one you swapped from.
The situation seems to me to come up through the recording process. If you select a program to record by "just" pressing the record button while on the channel that you want to record, it may trigger that "one moment please" problem on the other tuner, with the channels affected being the ones that you have most recently tuned to.
I have this theory because during the olympics this problem was popping up every night when I was trying to record olympic coverage just using the "record" button...I would find that I was then unable to watch specific olympic channels on the other tuner, they all had the "one moment please" message, and they were always the channels I had just most recently been flipping/cycling through watching.
Consequently, I never record a program unless I schedule it through the menu, I never use the "record" button on the remote to record anything.
As I said earlier, the only way I've found to get the channels all back on both tuners is to unplug then plug back in, this will clear those "one moment please" messages