Well, your issue a first!
What do you mean by "doesn't happen on my other boxes"? Do you mean other DirecTV Receivers? Do you hear the noise if you bypass the AV Receiver and connect directly to the HDTV? Just wondering if this is an AV Receiver problem. Hard to imagine why the DirecTV Receiver would do this. Is this happening on all channels? If you pause the Genie after you hear the beep, and rewind slightly, do you hear the beep at the same point in the playback?