The HDhomerun maintains the actual channel lineup internally and you can see it via the built in webserver.
Point a browser at the homerun's ip address and you will be presented with the main menu.
One of the options will be the channel lineup.
Click on the link and see if all the expected channels are there,
if the channels are missing you should contact Cox ,
if all channels are there, the problem is between the homerun and WMC.