If your EPUB's TOC is good, then when you do an EPUB to MOBI try the following settings:
Code:
Convert - StructureDetection - Detect chapters: /
Convert - TOC - Level 1/2/3 TOCs: all blank
Convert - TOC - Force use of auto-generated TOC: unchecked
I'm not sure whether the first two items are essential but I believe the third one is.