From tools … usermanager you can either choose “edit user” or “manage permissions”.
Under “edit user” you will find the GLOBAL privileges of the user, i,e, permissions that apply to ALL databases.
Under “manage permissions” you will find the SPECIFIC privileges of the user, i,e, permissions that apply to SPECIFIC databases.
In Mysql if the user has a global privilege to (for example) UPDATE, there is no need to grant right to specific privileges.
So check tools … usermanager … “edit user” – you probably will see the checkmarks there!