If I create a new product category I cannot then tick the sub-category box

Hey Millhilchapel

Can you let us know a bit more, are you doing this within Google Chrome as your browser? If not, try it with Chrome - it should allow you to select the box.

You have to create the parent category first, then the sub-category to attach too it. It won't let you select the box if it's the first category you're adding.