Hrm. For one thing, I think that the offsets NEED to end with a "0" for everything that's not the bones or first material, or else it may not work right. Shifting Jigglypuff's ear material forward by 4 bytes made it screw up. Don't tell me that's why Kit was able to work (all offsets ended at 0x#0) and Flandre didn't (all offsets ended at "0x#4").
Don't worry man, I'm almost done aligning the first material!
I have noticed that practically everything is aligned though...
Objects, Materials, Vertices, Normals, UVs, Colors, etc
Maybe that's the problem; the first material?
aww [censored] I hope it is lol