Ok, admittedly this is a very bizarre bug and there is a work around. I also don't think it's doing any permanent damage to the Spine files unless the file is saved.

I have a skeleton setup, where some bones have multiple slots on them (for instance, bare foot, foot with shoe, bottom of foot, etc). These slots are switched during certain animations. I've found that, while an animation is playing that switches these slots, if I switch Spine files, it can corrupt the setup pose under specific circumstances. This corruption will NOT be permanent unless you save the file

which could happen if you're not paying attention.

To reproduce (you need a skeleton with multiple slots on a bone that are changed by an animation):

1) Open uncorrupted spine file
2) Switch to "Animate" mode
3) Play animation that includes switching slots for a bone
4) While the animation is playing, click the Spine menu and open a different Spine file (click continue without saving, if the option appears)
5) Play any animation in the new Spine file
6) While the animation is playing, click the Spine menu and open original Spine file
7) Setup pose will show the slots that were attached while the original animation was playing. This will now affect all other animations

WARNING: do not save

I have added a couple of screen shots that show 1) the original setup pose, 2) the corrupted setup pose, and 3) the configuration of the slots under one of the bones that exhibits this behavior.

Is the setup of the slots under the bone ok? Or is that causing this weird behavior? If necessary, I can send the whole Spine file, but would prefer to do so privately instead of publicly on the forum.

A faster way to reproduce this bug is to skip steps 4 & 5 and just reopen the currently open spine file. This is just less likely to happen during normal use, I thought

EDIT: The workaround is just to reopen the spine file with the corrupted setup pose while the setup pose is being displayed. If you haven't saved the file, it will show the original setup pose.