Ok I think I figured it out!

Did you ever manually subscribe to shine or dak in the actual workshop?

If so you need to unsubscribe and clear out your files in your %\AppData\Roaming\Natural Selection 2 folder.

This way you ensure you do not have the mods and get them from the server. If you subscribe to the mod directly it will treat you like a server and give you extra files that are causing your problem.