when is Dolby 5.1 not Dolby 5.1

[shAf]

I watched an older movie last night (Circa 2006), what was the result of moving the main movie only to DVD (Nero Recode from Nero 7). The audio was missing many compnents that are there when instead playing the original DVD. The best example of what was missing was the movie score that is the backgound audio behind the final titles ... entirely silent!) ... but I could also barely hear similar score during the movie itself.

Did I miss a setting somwhere, whereby all 5.1 components would be guaranted to move to the "main movie only" copy? How can I avoid this in the future??

TIA