I can't believe this, but I had another oopsie.

[Amoné Fayden]

Jumping back to your main issue though, about not seeing some skins.
I would just go through your Base folder carefully and make sure you have no duplicate skins.

I've noticed since coming back that a few people are changing the name of their PK3 with different releases. Tergos springs to mind as an example.

Most people will click and drag the PK3 into their base folder and overwrite when it asks but if a PK3 has a new name then it will co-exist in your base folder with the original and cause errors unless you manually delete the old one.

In short:

Make sure you have no duplicate skins / old versions under different PK3 names.

[Sebastin Creed]

Indeed, this issue can also exist when using both base and RPmod folders.

For example, if I had one version of Amoné in my base folder - then started putting things in my RPmod folder, including a *new* Amoné skin, errors will start to come up and sometimes, if your like me, you may not think of checking both folders (on the off chance!) for a duplicate file kicking around.

So yeah, keep the folders tidy.