I've inherited a project v7.1.8 - the custom section(s) had been disabled to get the site live and now the client wants them.

In my dev copy, after a lot of swearing and killing caches, adding and fiddling with the configs (trees and application) and various other bits of black magic it finally appeared!

Then, after a couple of weeks I've come to deploy this to UAT. Same thing, I know the code is correct (and everything is named correctly, the usual source of issues) -I checked the trees.config, the applications.config all look fine.  I can even manually hit the custom section by putting in the URL directly but it failed to show up in the sections list (and therefore no user could see it). 

What I did was to add the permission to the SQL table directly for my user, you need to look up your user ID from the umbracoUser table and then add an entry to the umbracoUser2app table using the alias of your section ("application"). Then increment the ClientDependency and touch the web config, clear the cache, prey to the mystic Unicorn gods and, if you've been very good this year, the section will show up!

I sincerely hope this helps someone else. If not, it will at least come up in my Google searches next time I get this problem :)  I think my project has something in getting in the way (another ghost custom section or something wrong with Contour so this tip might be of limited use!).