I'm not sure what the problem is here, but if you can download the mobi file Amazon created for you, you can run it through Calibre (free program) and convert it to epub usually with no hicups at all unless you used some CSS directed at KF8 for Fire deivices such as drop caps. Then you can upload the epub to PubIt with no problems.
Thank you! I dowloaded the program and took a quick look at it. It's a little intimidating. I might be back with more questions, but thank you for heading me in the right direction.
It's what I call a "conversion" problem. Your file must be a certain format before you upload to a conversion program with B and N or Amazon, Smashwords, etc.
For instance: no use of tabs (indents must be pre-set in the entire document), lines should be 1 and 1/2 spaces apart, no fancy fonts, no use of headers or footers, no page numbers, no spaces at beginning of sentences, etc.
On their website, Smashwords has a guide for proper formatting of documents. It works for all conversion programs.
I don't know exactly what you've done, but you should "clean" your file before uploading again. See where you've done funky things and take them out.