I have the same problems that you have. My previous DVR had no problem with the IR emitter. I had lots of other problems and Time Warner told me my problems would be solved with the new DCX3400. Well I still have the same problems and my IR emitter won't work. After contacting Motorola who said all their connections on the back of the DCX3400 are enabled. Motorola says the cable companies choose which ones to disable. Time Warner points fingers at Motorola and my IR manufacturer. I don't know how they know who manufactured my IR emitter. I don't even know. Lot's of help on these forums. Some people mean well but don't have a clue. Some people even claim to have connections to a tech at cable companies but they're just blowing smoke.
Here are my conclusions: Your cable company doesn't want you to be able to watch and control your DVR from other rooms. That technology is in the box and when they enable it there will be an additional charge. They don't want you to be able to save programs to a stand alone hard drive because they own the programs. They don't want you to be able to use the firewire to copy programs from the DVR to a VCR or DVD because they own the programs.
Looks like I'll have to breakout old technology to make this work. Hope this helps!!