Hi Nate...
Simething that i checked is that the working atlas is like that(size=orig and offset= 0, 0 in everything):
skeleton.png
format: RGBA8888
filter: Nearest,Nearest
repeat: none
Head2color
rotate: false
xy: 2, 660
size: 302, 333
orig: 302, 333
offset: 0, 0
index: -1
Head3color
rotate: false
xy: 2, 325
size: 302, 333
orig: 302, 333
offset: 0, 0
index: -1
Ldaktylacolor
rotate: false
xy: 528, 69
size: 100, 60
orig: 100, 60
offset: 0, 0
index: -1
and the non working atlas is like that (size is dif from orig and offset dif from 0 , 0)
skeleton.png
format: RGBA8888
filter: Linear,Linear
repeat: none
Head2color
rotate: false
xy: 2, 698
size: 279, 324
orig: 302, 333
offset: 6, 0
index: -1
Head3color
rotate: false
xy: 2, 373
size: 279, 323
orig: 302, 333
offset: 6, 0
index: -1
Ldaktylacolor
rotate: true
xy: 144, 2
size: 85, 39
orig: 100, 60
offset: 9, 8
index: -1
Thank you