Hello JoeTheHunter,
I'm currently on holiday till the 14th, but I'll help you with this.
Have you set the data within the Body Sprite Setter as well?
I've attempted to replicate your issue, but it is working as intended on this side.
Are you sure all data is set correctly? Such as the sprites. Note that it is important that all sprite names should stay the same when creating new textures. (I've created a tool for this to make this less tedious, scroll down)
Sorry that this isn't documented but there is an easy tool available within the package to slice up and create new data files.
Only thing you would have to do is duplicate the pants image and go to:
Assets -> ScriptableObjects -> Character -> Generator -> Character Part Generator.asset
This will automatically slice up the texture for you, just ensure it has the same dimensions as the other pants images. It will also ensure proper naming. This will save a lot of time for you. The processed image will be placed at the same location as the Character Part Generator.