Have you checked the Disc # number field values? Internally the disc numbers are included when files are sorted by track numbers.
For example:
1st disc 1, track 1
2nd disc 1, track 2
3rd disc 1, track 3
4th disc 2, track 1
5th disc 2, track 2
6th disc 2, track 3
7th disc 3, track 1
8th disc 3, track 2
9th disc 3, track 3