Here are the workarounds. I have the same tuner and used to have Direct TV. The remote does work for everything but Live TV. You have 2 options:
1. You can purchase a new remote that has an IR Transmitter that you sit in front of the IR Receiver on your set top box. When you change channels on your remote, it sends a signal to your box that changes it's channel. Then you are able to use the guide and have every channel your set top box has.
2. You can run your coaxial cable into your set top box then back to your computer. Then in media center, set it to channel 3. You can change the channel with your set top box remote, but you cannot use the guide in media center to record future shows
Then you can run your AV cable from your set top box to your TV and have both going at the same time if you wish.
Direct TV does not current support hooking the coaxial cable directly into the tuner.