I have had a similar problem twice recently.

Originally, my problem was a very slow "wake up" on occasion.
The ProntoTeam suggested a complete re-load of the OS.
I followed their instructions, and that solved the problem,
but meanwhile, a symptom similar to yours has started.

After running a "all lights off" command that waits one
minute for me to leave the room, the remote just stays
On. The screen remains lit, and no buttons seem to work.
This continues until the battery runs out. After charging,
it returns to normal operation, but then it'll happen
again when I use that function.

I'll try the above suggestion this weekend and report
back.

At least the slow wake up is fixed. That was really annoying.

-doug-