@LZL Sorry that Spinebots answer is not quite matching your problem, it unfortunately can't process images (yet). The lower half however might still be useful, so I'm leaving it as-is.
As your skeleton also shows incorrect atlas regions, and alternating outline- and normal materials:
- What does your initial skeleton setup look like material-wise?
- What materials are active before repacking?
- How did you create the outline setup on your skeleton before repacking?
- What render pipeline are you using? I assume you're using Built-In Render Pipeline, is this correct?