Originally Posted by booklover6
Maybe it is messing with the section order. I use Sigil on every book before I load it, to take out all the extra images at the ends of books, teaser chapters or excerpts, advertisements, etc. So I convert to epub, use Sigil, then convert back to mobi, before putting on the Kindle.
I'll play with merge again and see if that is the problem.
Do this Convert the Sigil epub to a Calibre epub then try to merge. My guess is Sigil could be messing up the navigation file. Running it through Calibre first before merging should fix it.