BuddyPress.org

Did you follow the part titled “Advanced Optional Step: Removing the database tables”.

That is the key to your question. The settings are all stored in the database tables. BuddyPress does not have an option to purge the database settings upon deactivation. You have to manually delete the tables.

Be careful! You could screw up your whole site if you remove the wrong tables. Definitely back up your database before attempting any of that.