There is no reason you shouldn't be receiving the non-HD channels with an HD box. What are the symptoms? Do you get a message, or can you just not tune the channels? It doesn't make sense. Have you called Comcast and asked them to send a hit to the box?
I went through and reduced the number of splitters from 3 to 2 and now I can receive the non-HD channels. Not sure if that made the difference, but it also helped the quality of the HD channels.
FYI you cannot go willy nilly changing out splitters here and there. If you have a signal degregation issue you need to get a tech out there to troubleshoot the issue
