Which system do you use?
HD Channels need AC3 Support, does your XBMC Setup support AC3?
I am not entirely sure but usually HD channels also deliver MP2 Audio channels, you possibly might have to change the Audio channel in the tvheadend setup (I didn't do that myself yet because we never experienced such issue yet).
It's working with some HD channels including with AC3 audio xbmc doesn't shows audio tracks in the problematic ones.
I think it's some related to how channels.conf was generated.
Looking at channels.conf w_scan has generated, I've found that the channels without audio doesn't have APID set up like the channels with audio:
Without audio : FOX HD;(null):267000:M256:C:5217:2320=27:0;2321,2322:0;2116:1861,1802:631:2:40:0
With audio: ESPN HD ;(null):129000:M256:C:5217:1056=27:1057=eng@4;1058:0:1802,1861:571:2:35:0
I'm using VDR 2.1.6 + VNSI Server 1.2