I was gutted when I got the DVD's and noticed the beacon's soundtrack was different to the movie
There are a couple of others, as you quite rightly pointed out, and that's annoying me also.
On one of the commentary tracks, Peter J mentions people can edit the film into its chronological order these days at home. Quite an interesting idea, but I am considering editing the soundtrack, mixing in the missing themes and burning back out to DVD
The beacons bit really hacked me off, its nowhere near as impressive in the movie - why was this changed I wonder? its not just a different mix or levels, its a different arrangement. odd.