The PCM/Dolby option you mention only works for the tuner. If your input is HDMI as you indicate, it has no effect on it and therefore is grayed out.
Try changing the Source to TV - you should now be able to toggle between PCM and Dolby, but again, this has no effect on the audio from other inputs.
I just recently purchased a samsung ln46c610 lcd tv and a bd 5500 bluray player. I have them connected together via hdmi with an optical digital out to my JVC home theatre system. The probelm is , on the tv set for audio, it is set to pcm only and the dolby is grayed out. I al so trying the bluray player to make sure it was dolby out. I contacted samsung support by phone and they tried a few things but to no avail. I am getting HD tv this week via cable and will try using that system as something to output digital dolby to home system. The home system does dolby and DTS and worked fine on the older DVD player i used. Cany comments or support is welcome!!