Sometimes people experience discomfort from a temporary crown for a variety reasons including some pulpal inflammation or irritation due to the drilling, poor fitting temporary crowns, etc.
You can have the permanent crown cemented permanently but you can also discuss with your dentist the possibility of replacing the temporary crown to see if it may be a bad fit or some other underlying problem. You can also temporarily cement the permanent crown with a temporary cement but sometimes it is hard to get off and can crack or break when trying to remove it which may start the process over again. Your dentist or you may not want that though but its an option.