Yes, this one is on the internal bug list. Newly added songs re-use old FIDs, and because of a bug, they inherit the statistics of the last song to carry that FID.
All of the statistics are from the scratch partition, and they are all from the old FIDs, and since you did a complete re-do without erasing the scratch partition, they're all changed around.
One way to avoid this is to run the builder image on your player and reinstall beta 13. The builder image will completely reformat the hard disks, including the scratch partition, and allow you to re-add your collection fresh, with all zero values for all of the statistics. If you want to go to that much trouble.
If I recall correctly, I think Mike Schrag is working on a way to get Jemplode to edit those values, although I don't know if that's in the current version yet.