I think that the 2003 DVD Special Edition introduced changes to the soundtrack which were carried through to the Blu-ray. You have to get the LD PCM to hear the original version... HDNet Movies ended up broadcasting the original mix. That's cool, but what I found strange was that HDNet broadcast it in 5.1 because I had only ever heard the original mix in 2-channel.
The differences are as follows:
1. Snake says, "That's real good" after Cabbie says "He's A Number One..."
2. During the assault on the station wagon as Snake drives down Broadway, there is now music played all the way through the attack. Before it was silent except for the barrage of the crowd.
3. Brain's line to the President is an alternate take in the new mix... "God Damn Redskins! They're savages Mr. President!" You can clearly hear the difference between each mix.
There could be more but I think that's the major stuff.