Have a Direct TV remote, Toshiba TV and Direct TV box. The remote works with the box, but I can't program the TV. I select the TV mode, switch the mode to TV (green light flashes) and hit mute & Select buttons. It then tells me those buttons aren't programmed. Of course not - that's what I trying and failing to do!
Mine did this and I went into Program Remote. Where I was to put in model of TV (mine is Sanyo 50842) I selected Sanyo and instead of inputting my model number I scrolled all the way to the end of the 650 or so models and selected "model not listed" even though it was. That did the trick! Good luck.