https://giant.gfycat.com/BreakableDefensiveGoldeneye.webm
I used to have this problem with the second axis of the shear attribute, but now shear is working fine and the it's the right scale that I'm having trouble with. I haven't opened Spine in a while, but I use scale much more than I use shear, so this is going to be very annoying.
This only seems to happen when world space is selected.