Atlantis, I read, can generate two different TOC's: The one that shows in Adobe Digital Editions, on the left side, and an HTML TOC, that will show as a page.
The first one, you have little control over. The second one is placed in the epub file along with your text files and can be edited (eg. with Notepad) to your liking, AFTER the epub is generated.
unzip your epub and see what it consists of. That clarifies a lot.
It's a common problem with these fantastic systems that promise to do everything for you: the downside is, that you lose control.