Clear QAM channels are scanned using the QAM Standard, QAM HRC, QAM IRC, QAM HRC + 3 and QAM Std Alternative tuning detail files.

The frequencies listed in those files should match the details here:
http://en.wikipedia.org/wiki/North_American_cable_television_frequencies
http://www.jneuhaus.com/fccindex/cablech.html

The "odd" (exceptional) frequencies are documented here:
http://www.gpo.gov/fdsys/pkg/CFR-2011-title47-vol4/xml/CFR-2011-title47-vol4-sec76-612.xml

Physical channel number is taken from the index of the frequency in the file. So for example, the first frequency is channel 1, second is channel 2 etc.

Extra frequencies in the files is leading to incorrect physical channel number assignment.
Also, some of the exceptions in the link noted above are not accounted for.