Hi guys, Same exact issue here. In my case, basic system with a MRF260 and a MX350. Same dead buttons as Joe R mentions above, although I never got "exit" to work. If you take a look at the window of the cable box with a flashlight, you'll see that the eye is all the way to the left but it's set back and sits in a channel of plastic. Best spot for the flasher is directly on top. Honestly I don't think that it's the issue. It has something to do with the way the box sees the codes.

To start we used the standard comcast "110" code set that works on every other box. That gives you about 50% success. The rest of the buttons cannot be taught. Codes still don't work. Obviously its the same code set but the box must some how see it differently. I say that because there is no way that comcast would change remotes and then depend on there people to hand the correct remotes over. So the problem lies with universal communicating to the box.