I don't do Automatic TOC generation as I think it's flakey. Doing a search for TOC problems here and on the Adobe Forums proves it.
I always do the TOC linking manually after I've made the epub. By unzipping and editing the toc.ncx file.
e.g.
Each entry in the toc is listed like this:
<navPoint id="navpoint-10" playOrder="11"><navLabel><text>Chapter_05</text></navLabel><content src="Chapter_05.xhtml"/></navPoint>
So all you have to do is move the </navPoint> around to create the TOC levels.
Title page </navPoint>
Part One
Chapter One </navPoint>
Chapter Two </navPoint></navPoint>
Part Two
Chapter Three</navPoint>
Chapter Four</navPoint></navPoint>
Which will look like this:
Title page
Part One
Chapter One
Chapter Two
Part Two
Chapter Three
Chapter Four