What is happening here? Tracks missing, tracks in the wrong order, arewe talking 2 different nights then? Looks likely.
Perhaps we ought to make our own compilation - with all the material.
The DVD is based on a single performance, originally recorded as a pay-per-view TV show. There have been little fixes here and there, but it's allegedly fundamentally just that show. I don't have a copy of the original PPV, but completists probably should.
The CD is a compilation of dates from England, Italy and Germany. Allegedly there are no overdubs at all, though there are cases where a single song is patched together from multiple sources in an attempt to create a single "perfect" version.
Fans with a much greater obsession (and bigger 1994 bootleg collection) than mine have compiled a list of what was recorded where at the bottom of http://pinkfloydhyperbase.dk/albums/pulse.htm.
I don't think the tracklisting of the DVD has been altered in any way. The 1994 laserdisc did shuffle some songs around in order to fit the entire thing on three sides without a break in DSOTM.