I just updated to 0.9.3 but am still having problems with the conversion AZW3 --> (old) MOBI for my Kindle, as far as TOC is concerned.
For some, but not all, books the TOC is generated, but even in the calibre viewer one can not navigate it by clicking on the chapter entries in the TOC.
I tested the AZW3 files in the viewer and those links do work (i.e. I can navigate the TOC). In the MOBI files most of them work, but I have examples in which they do not (none of the chapters). I even have one book in which the MOBI TOC works partially: the first 3 chapters and the last two are active, but nothing in between.