Hey,
Things I can recommend trying out:
1. Validate the game cache with SteamCMD
2. Check the database with
HeidiSQL for example and look for entries you don't want (Make sure to do this when the game server and web server is down though - so the server won't overwrite the potential changes).
3. Type "sm plugins list" to make sure all plugins are completley gone and not loading.
No idea if them things will help, but no harm giving it a try.