I work for Charter and although I'm not the "headend guy" I've done my fair share of work in them. As for your analog channels, the audio carrier has to be -15 dB below the video carrier level which is your a/v ratio. The actual audio level (which is easily adjusted for analog anyways) is simply determined by ear throughout the analog bandwidth. The levels are set at a happy medium so as to not overdrive the modulator which often times will unfortunately be significantly lower than the digital channels. Each analog channel has its own reciever and modulator. For each off-air channel you simply have a demodulator and a modulator. You can control the off-air audio levels to some extent but they are ultimetly determined by the broadcaster. Then you have your digital channels! They are recieved in "pods", multiple channels with one reciever. (One analog channel one reciever. Ten digital channels , or more, one reciever). Then all of the recievers feed into a "modulator". For instance 80 channels, 2 "modulators". Everything is compressed and not so easily controlled. For the most part most channel audio levels are based on the off-air channels because of the limited adjustability and the widest subscriber base. Analog channels are easily adaped to any level but with low off-air levels and generally high digital levels there's bound to be some difference.
I have my basement setup through a typical 5.1 which I always use in 5.1 and my audio levels don't change. I then have my upstairs setup which uses a 5.1 that triples as a digital cable box, dvd player, and 5.1 all in one box. When I listen through just the tv, there is some change but not alot. When I listen through the 5.1 however the digital channels versus the analog will farkin blow you out! Needless to say I use the tv speakers for tv viewing.
I admit the cable companies do have issues with their levels but we do do our best. Try playing with different types of cables and your stb should have some settings as well.
If you have any other questions I'd love to try and help, hate to have an un happy cable customer!