Ah, this should be a pretty simple fix! I believe I understand the issue looking at the two images. The cause is likely a conflict of some kind with the char_swatches_lit_m present in global.p3d. The game keeps multiple copies of that texture around, and while this normally isn't an issue with the vanilla character models, it causes tons of conflicts with custom ones that make modifications to it. Lucas' P3D Editor displays the model just fine since it only loads the one referenced in global.p3d and ignores ones you'd see buried in a Level's TERRA file.
My recommendation would be to rename your char_swatches_lit_m Shader to something unique (such as 'sonic_swatches', as an example), and then also accordingly change the references to it in the character's 'Skin'. An example of that would be something such as this.
Hopefully that resolves the issue.