This is just a guess because I haven’t tried it yet, but you may need to add new meta_keys to the usermeta table for each secondary WP install.
Say a secondary WP install uses the prefix wp2_, add the meta_keys wp2_capabilities and wp2_user_level using the same user_id and meta_value values as the adminstrator for you primary WP install.
Like I said, this is just speculation, but I will be trying it soon myself. Let me know if it works if you decide to give it a shot.
