vBulletin is worst when it comes to upgrade. It involves a lot of manual work and things always go wrong.
I upgraded vBulletin forum to 4.2.0 from 4.1.8 and Navigation Manager was messed up.
When you click on Navigation Manager it shows Page Not Found.
I checked the database and I could see navigation table. So it seems database has it but for some reason it doesn’t show up.
A quick Google search couldn’t show any clear cut solution.
The next step was to re-upload all files and run the upgrade again. This still didn’t solve the issue.
I still can see the navigation table in database.
Then I decided to check the folder structure and while doing so I found the problem.
I had renamed the admin folders for security reasons and that is why the upgraded version couldn’t take the correct folder.
I fixed the folders and it worked.