Hi. Let me see if I can help.
Even for products that I own, I like to get the electronic version of the manual because I can search it much more easily. You can get the owners manual for your blu-ray player on the Sony website, with the direct link to the PDF file
here.
Check out page 22 of the manual. If you haven't already, set the "BD Audio MIX Setting" to "Off." If that is set to on, then HD audio won't be output through bitstream. That doesn't entirely match your original description, but it might be it.
Btw, you asked originally if it might just be the disc. Have you tried more than one since posting that?