The 45-track version is clearly legit, and what I think happened was that they basically just dumped all the tracks as they appeared in the game onto a CD (the same happened with Morrowind.) If I recall correctly the number of tracks and the names match exactly with the data files.
The source of confusion with the track lengths is that I believe they messed up and put them in the wrong order on the CD (or listed them in the incorrect order on the back.) I found
this thread where someone listed the correct track order. If you look at the link, track 1, which should be "Main Theme" (2:31) is actually track 37 "Battle Dungeon 3" (1:32) and so on.
So as far as the actual track lengths are concerned, the previous list was probably correct, but the order of the track names was not (unless you go strictly by the back cover, in which case the incorrect might be correct, though it doesn't actually specify any track numbers.)