SMAPI says I need to update mods I've either already updated or no longer have

I've updated SMAPI for the 1.5 release and I updated all my mods off of Nexus. Upon launch of the game, however, I was notified that my mods were skipped and that my mods could be updated. I deleted the content from my mods folder and re-downloaded everything and still had the same issue! It was also giving me notifications for mods I no longer actually had installed. I've tried everything short of uninstalling the game at this point and I'm at a loss as to what I can do to fix this so my mods can be played. Anyone have a fix?