OK, trying to narrow the problem down a little further I decided to go and try some of my older mobis that I know used to open right where I wanted them to. I figured I might be able to narrow the problem down to when I switched to a certain new verision of Sigil or Calibre. Guess what, all my old files that used to work just the way I wanted them to now do the same thing as my newer ones. They open to the heading/first nav point in the ebook. It's really starting to look like my Kindle is the issue and not Sigil or Calibre. It seems as if something changed on a recent firmware update that is causing this but I have no idea what or how to correct it.
The whole problem is very strange.