From my analysis here:
"A Conspiracy Unmasked" or Analyzing the Fellowship of the Ring CR - General Discussion - JOHN WILLIAMS Fan Network (
http://www.jwfan.com/forums/index.php?showtopic=23818&page=1)
Comparing the Lord of the Rings Symphony CD to the OST/CR
DISC 1 MOVEMENT I
The Prophecy/Prologue: One Ring to Rule Them All (Original Version)
Pretty much the same content as the OST track, however 1:02 of the symphony combines the Cor Anglais from 3:58 of the Rarities version of the Prologue and the horn from 0:58 of The Prophecy on the OST.
The rest of the prologue portion of the movement uses the film version.
Concerning Hobbits/The Shire - Bag End
The symphony version is slightly shortened.
The Treason of Isengard/Three Is Company
The Seduction of the Ring is sung instead of hummed.
The Journey There section is omitted, instead the music transitions to....
The Black Rider/A Shortcut to Mushrooms
The brass at 0:40 of the OST track is not in the Symphony version.
There is music not in the OST track at 9:03 of the Symphony version.
At 10:22 there is an additional descending horn line, however it is mixed very low, it can be heard more easily in these videos:
At 9:52:
https://www.youtube.com/watch?v=ybZINoDv8I8
At 1:47
https://www.youtube.com/watch?v=g9RMZbNu3So
Instead of resolving with the last note, the music instead transitions into....
The Treason of Isengard/Saruman The White
The Symphony uses the OST version.
END OF MOVEMENT I
MOVEMENT II
Many Meetings/Rivendell
OST Version, transitions to...
The Ring Goes South/Gilraen's Memorial
EE Version, transitions to...
A Journey In The Dark/Moria
More prominent (extra?) Khuzdul singing, and harsh instrumentation, the Live to Projection version is similar, but less harsh.
The Bridge of Khazad-Dum/Balin's Tomb
Uses 5 seconds of percussion similar to the clean opening of the Fellowship theme for the escape from Balin's Tomb.
Lothlorien/Caras Galadhon
Seems to be TE and EE version hybrid, contains clean ending of "Lament for Gandalf"
The Great River/The Fighting Uruk-Hai
EE/OST Version Hybrid, contains extra music at 21:54.
Amon Hen/Parth Galen
EE Version
The Breaking of the Fellowship - May It Be/The Road Goes Ever On Parts 1 and 2
OST version
END OF MOVEMENT II