Mobipocket Creator does the best job on converting PDF to mobi, but I just couldn't bring myself to go back to IE 8, which is what most of the answers seemed to suggest. I gave up for a few months, but today I had a huge PDF with a toc entry for every other page so googled again so I wouldn't have to manually add the entries in Sigil.
I tried your fixes and voilą! I'm a happy camper again. Thanks so much for tracking this down.