I know this is old but I found this from google, in case anyone else ends up here, I renamed my Mods folder in here
C:\Users\%username%\AppData\Local\Larian Studios\Baldur's Gate 3\Mods
and that fixed it.
some one of my mods was having duplicate IDs, the toolkit seems to load all the mods there instead of what is chosen so it's pickier then the actual game.
https://steamcommunity.com/app/1086940/discussions/0/4758704179140788572/
