Tuning in the cable channels with digital equipment seems to be kind of hit or miss. While scanning for OTA signals takes maybe 10 minutes, scanning for Cable takes a good half hour. During that process the tuner tries to eliminate all encrypted signals. Sometimes it can be a bit tricky to determine which of the signals are encrypted and which are not. This can result in missing channels.
Some digital tuners find all the channels, and then go back and eliminates the scrambled channels. Others tuners do this in one pass. The two step tuners like the Samsung find more channels than the one pass tuners, especially if you interupt the removal of the scrambled channels, and then eliminate the channels manually.
Do a factory reset of the tuner, and scan again. Make sure you are set to Cable before you do your scan.
My tuner starts finding cable channels when it reaches channel 68. If I time the scan so that the tuner reaches channel 68 just after the commercials end, I pick up more channels than if I am at the populated channels in the commercial time.
Also Samsung does the cable Analog/Digital all in one pass in one pass. My cable company sends local out in analog and digital for the locals. If you OTA channels are missing, then it could be that your cable company is only doing QAM for some of the channels and the analog channels are not getting passed through.