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I have no idea why that's happening then. Maybe try unsubscribe and then resubscribe.

Beyond that I'm unsure, you could try extracting the mod into whichever mod you already got working.
 
I managed to fix my issue by going into Documents/ParadoxInteractive/Stellaris/mod and deleting every file that didn't start with 'ugc'. So if anyone else has the same problem, that's how you fix it.
 
Then it sounds like you maybe had a mod named the same in the Mod folder? Those takes precedence over workshop mods, so if it was empty it might replace the workshop version with one that didn't work.