I'm having the exact same problem on my Sony BD player with disc 2 of the Two Towers blu-ray extended edition! The Sony BD player doesn't recognize the disc - it says "unknown". Did you find any solution to this? I contacted Warner Bros - no response. Has anyone tried talking to Sony?
Just fyi, I had this problem with disc 2 of Two Towers on my Sony player just recently. Disc just loaded endlessly. I thought the disc was defective at first. Turned off my internet connection and the disc played perfectly.