[Lynne]

Rebuild User Reputation
This function recalculates user reputation using the value that you specify below then adds the total reputation the user has received so far. This will remove any custom reputation that has been given to the user through the user editor.

That should rebuild your Reputation Level which is a number based on all the reputation that is given to the user by others. There is also the users Reputation Power which is how much reputation he can give to others. Most of the stuff under AdminCP > Settings > Options > Reputation Options, like Register Date Factor and Post Count Factor, etc, have to do with the users Reputation Power (how much they give), not their Level (how much they got).