Menus not showing up

There are a number of issues about this but none that address my particular issue. I have Coraline as my theme. I had some problems with linkages not occurring and in the process of fixing that via the manual upgrade, the menus that are not the Primary Nav are not showing up. I have had my host restore from the day before and from the weekly backup and nothing has fixed this. The menus and the 100s of pages under them are still in my dashboard so they are not lost, just not visible. Any help will be appreciated. Thanks!