I was having the same problem with my SB-HD, and then read a post somewhere else commenting that one should setup the coax connection to the clear channel coax cable inputfirst on the SB, before seting up any connections to component cables or composite cables, etc.
Since I had already done the latter, I unplugged the AC power to my SB, unplugged all cables, then plugged in ONLY the clear channel coax cable to my SB and did a hard reset to setup the SB from scratch. I was then able to get the clear channels registered. Then turned off the power to the SB again. Plugged in the cable box and composite connections I had been using before, restored power to the SB, and then ran setup again for the cable box supplied channels. Now, eveything works fine.