I had the same issue with Pink Flyod - The Wall it kept playing CD1 track 1 >> CD2 track 1 >> CD1 track 2
Track / file named according to the CD side 1-01, 1-02 etc. 2-01, 2-02 etc.
But the key is the actual track number. (# under properties of the file)
I simply changed # for side 2 to from 1 > 201, 2 > 202 and now it's playing all tracks on in the correct order.
Otherwise the suggestion about the iTunes tool from the syncmyride site works for missing tag informations very well.