Okay, I have not found a way to generate a solid table of contents.
However, I have found a way to stop the crazy scrolling.
Where #jump_page is defined in docco.css, change it to :
#jump_page {
padding: 5px 0 3px;
margin: 0 0 25px 25px;
max-height:750px;
overflow: scroll;
}
I then took my altered stylesheet and passed it in instead using the docco css option.
It's not the best solution, but it will set a maximum height and allow scrolling, so if you have a plethora of files you want to document, you can navigate them more quickly.