It does sound like there is something odd about the pdf. As I said, handling of pdf's on the Kindle is not perfect, but I've never seen the problem you describe before.
For conversion, there are at least a couple of options to try:
If you use the email method of getting the document to your Kindle, you can put "convert" as the subject line of the email and Amazon will convert it as they send it.
You didn't say which programme you've downloaded for conversion, but the most versatile ebook management/conversion tool is probably Calibre (
http://calibre-ebook.com/).