I think a clock problem would stop the sound going to the master fader but it wouldn't stop the VU's from showing. Is your clock showing locked from your HDR or visa versa.
Are you sure you have your light pipes going in the right holes? What is your clocking situation between the two devices? I know it is probably not likely but make sure your HDR is setup for opt and not TDIF in the HDR setup window. If you are running OPT.8 cards, it won't be an option but DIO.8 cards gave you the choice.