When first got FIOS, the remote would not work for my multi room DVR in the media room. I switched boxes and remotes with the upstairs box. They worked flawlessly when upstairs! Then I read somewher that the lighting in the room affects the remote signal. Put a Post-It over the IR on the box. That's ridiculus. But..IT WORKED!
To test, turn the lights down or off in the room with the un-responsive box and see if the remote works. Drawback s when I turn the lights down low to watch movies, I need to remove the Post-It for Box responce, but thats rare