The problem "probably" lies in the source html.
To create good well formed mobi in calibre you are best to input a "default" epub doc.
Try...
Opening your html in Sigil and then save as to create an epub. Break it up into chapters (there's a guide somewhere on the forums, just search it - Rough guide Word to mobi..I think,) The very first file should be your cover and it should be *.htm not xhtml. If it is not, create a new break at the top of the htm page, if you want to keep it, rename it the same as the first xhtml file ( add an "a" to the end). Now import your cover image to the htm page, save. Check and tidy your epub, generate a nice clean TOC/NCX, and edit as required, then and use calibre to convert the epub to to mobi. Remember to tick the "Put TOC at start" box.
You should now have, cover, TOC, title page....etc.
Good luck.
