I had an issue with a remote that didn't work and followed the instruction that DTV provides and the next step was to order a remote. I never give up so I went to the other box I have and pulled up the menu to read about setting the remote from RF to IR or vice versa and there is what it said and what I did.
Hold the select and Mute buttons till the light blinks twice.
Then type 961
Then push down to choose the remote to go to IR mode
Then press enter.
IT WORKED!!
I'm thinking maybe the RF in the remote doesn't work or in the other box, not sure but this works perfect and should be provided as a step before buying a remote. I tried programming it for RF and it doesn't communicate in that mode but it's fine now in IR.