This could be caused by a weak signal, which can affect only certain channels. Check the connections to the cable box, especially the incoming coax, and eliminate any unnecessary splitters.
To check signal strength with a Motorola box, tune to the offending channel, turn off the box with the remote, then within two seconds hit "OK/Select." This will bring up the diagnostics screen. Select "Inband Status" (probably page d04) and look for "SNR" for the tuner(s). This value should be in the mid to upper 30s. You may be able to improve the signal strength by adding a signal amplifier to the incoming cable line.
You could use the remote's "swap" button and set each tuner to the same channel. It would only be useful if you think one tuner's signal is significantly weaker than the other. If you're trying to compare signal strength between two channels you can get both values at the same time by setting each tuner to a different channel.