This is not really a serious problem, but you might wanna fix it at some point.

When loading up a fresh config file, all the worldgen is not showing under the worldgen category in the config file (Which i'm pretty sure it should :p ).

Config file, pastebin: http://pastebin.com/h3L4tx4q

I don't really see a problem?

That's just how it's layed out. intentional