I had a similar situation when I set my HTiB up the other day. You need to connect your receiver to your tv via an optical cable and if it's a Samsung unit, you have to turn off the ASC (Auto Sound Calibration). Then you can select your 5.1/surround mode with your Dolby ProLogic (or similar)...
I know I'm kind of late to the party on this, but I found this thread/forum while searching the net for the same problem. I just got this system too and experienced the exact same problem. I solved it by connecting with an optical cable (I have a Samsung LCD that supports this) and one other...