I don't doubt that things may have gone wrong in some instances. But I didn't notice any such errors in the few works on freekindlebooks.org that I quickly looked through, so I can't evaluate what exactly might have caused the problem or how it might, if possible, be corrected. Are there particular instances you might be able to point me to?
Sorry, its been too long, I don't remember where. But when it goes bad, it goes very bad. I think I remember among other things this algorithm (embedded in GutenMark) goes horribly wrong on running long quotes (as do most algorithms.) Also unrelated it screws the pooch needlessly on left single quotes -- it appears to try to implement them using "ASCII" U+0060 At the time I was using Gutenmark to "quick and dirty" get to HTML at a time when PG was still offering some texts txt-only.