Try starting from a New Game, and it may fix the issues.
The Type info and Data of the Variable DB is transferred into the Save Data at game start.
So, if you make changes to the Variable DB’s Type Settings or Data in the Editor, and then continue from old Save Data, it will try to load from a DB unaffected by these changes, which can result in data counts not matching up and data being out of date.
Note that the User DB and System DB do not depend on Save Data, so problems of this sort will not happen with them