this seems odd to me. and hard to describe, too. here goes:
i convert to epub a nicely formatted file, but that doesn't have a toc with the express purpose of generating a toc. when i open the epub in sigil:
1. sometimes a toc appears in the right window (good, all done)
2. sometimes there's no toc in the right window, but there is one set up in the toc generator window. (tell it ok, good, all done)
3. sometimes neither of the above happen and i must tag the chhapter headings by hand. (slow and tedious, but ok, good, all done)
4. sometimes the same as #3 happens, but when i put my cursor next to the chapter heading text and click for a level, nothing happens. often this happens on odd numbered chapters whereas the even numbered ones create fine.