I have blocked nearly all channels that don't come it perfectly 100% of the time. In this case, I find that the blocked channels remain blocked, regardless of what additional hardware scans might pick up.
@CScott, you are getting channels with poor quality and strength. An basic inline usb amplifier would pump up the strength to 100% on all of the channels. And then to maximize signal quality, possibly an app like signalgh would help to get your antenna in the best position, as you can see the signals in real time and don't need to lock tuners to check the stations. (an alternate and slower method would be to just repeatedly refresh the tuner status pages on your HDHR while tuning channels on your tv and moving the antenna).