I know this might sound stupid, but are the internal switched on your roof mounted antenna setup for the system you're trying to use, i.e. Dish or DirectTV? I saw your post on a diffrent forum and just now wondered if this might not be the reson you're only getting part of the channels?
2012 Winnebago "Journey To Insanity" 40U
2008 Dakota Sport 4x4
2004 Subaru Baja - DW's
2006 Honda Shadow Aero - TOAD for now.