Works now Jimm, thanks. And seems that you are right, I thought it would be a matter of modifying the TOC html to contain a <div id="toc"> tag, but apparently that is stripped during the epub->mobi conversion... if one could prevent Calibre from so aggressively stripping all these tags it would probably work, but alas I haven't found the correct option.
EDIT: It seems like the table of contents is used when I convert the epub to azw3 instead of mobi. Or not, oh well, it's too much of a hassle for such an unimportant feature.
Last edited by cryzed; 10-03-2012 at 02:34 PM.