Oh, ugh. Your post takes me back. I had similar problems with my first Kindle upload. I finally solved it by converting the doc to HTML and manually inserting begin paragraph HTML marks and end paragraph marks throughout the entire document.
Anyway, since I never want to go through that again, I've been looking for ways to keep the process simple. And as the original poster suggested, that lies in formatting the original document correctly. If you manage that, you should be able to upload the doc without doing conversions through other programs.
The advice I've found helpful is to go into Paragraph, then Line Spacing Options, and Indentation, Special, Line Spacing Options, and set it at 0.20." Then as you write, each paragraph is automatically indented. Trust me, setting this up correctly in the first place is much easier than going in HTML and inserting all those paragraph marks.
I would think that by highlighting your paragraphs, perhaps by individual chapters, and applying the above paragraph settings you may be able to straighten out the errors. Also, there's Mark Coker's advice for setting paragraphs which is to use the little arrow thing on the ruler. Anyway, I think if you can produce a clean doc copy, your upload to Kindle should go okay.
I do wish you luck. My efforts to clean up my original smudged copy nearly drove me mad. But my copy was corrupted because I'd lost my original version of the novel when my computer crashed. So there's another warning. Always keep a back up copy of your work.
Anyway, good luck!
Last edited by Anna Drake; 01-24-2013 at 02:23 AM.