I've noticed exactly the same thing, icehawk21: my 990's volume control has to be set 10db higher on the HD channels to get the same listening levels as on the non-HD channels. But I can't see how the 990, or any other preamp, could be doing anything with the signal it receives that would cause this - or control it either.
I think your question should be directed to your local cable provider. I haven't yet asked mine (Cox Cable) but maybe I'll do it now. Maybe we all should if we've noticed this volume shift - let the cable providers explain this to us, or, better, change it.