Issues with order and size of character sprites

[TerraBubbles]

Hello there, I've been browsing the forums for about a week now looking for an answer to this and haven't really found a reliable one. The layer order of sprites doesn't seem to be changing in game. I have tried to adjust the z order in spriter, edited the z order in the scml file, and nothing has worked. Attached are photos of what the sprite is supposed to look like, and what it actually looks like in game. 

I also just tested putting a hat on my character, and the last photo is what happened. I was messing around with the size of the full body using this code, placed in the prefab character.lua file under the stats section:

inst.Transform:SetScale(1.5, 1.5, 1.5)

The size looked fine to me using the 1.5 scale, and I have no idea what happened with the hat.

Thanks in advance for any help!

[science scout]

I had this problem too when I was trying to get a skeleton sprite for my pirate mod I was so confused  when not only the eyes are out of place but the images were overlapping too he works as intended in-game tho