BBC HD and ITV HD broadcast using Dolby Digital audio (either 2.0 or 5.1) whilst the other SD services are broadcast using MP2 audio. AIUI the way Dolby is handled by Media Center and Windows can be different to the way MP2 is.
If you bitstream DD to an external amp then your PC can't alter the volume (it would have to decode and recode the audio to do so) - but ISTR that in some (all?) cases even if you decode in your PC then there are also differences in how audio volume control is handled.