Your post probably belongs in one of the ebook software forums, perhaps in the Calibre forum. I use Calibre for my conversions and it allows you to modify paragraph spacing in most formats. I never convert to PDF because I hate the format so can't give more specific advice on converting to PDF.
Here's the Calibre help section explaining format conversion:
http://manual.calibre-ebook.com/conversion.html#.
In general, go into preferences - change caliber behavior - conversion - common options. You'll find an option that allows you to add or remove spacing between paragraphs. I hope this helps, but again I don't ever convert to PDF so can't really tell you much about PDF conversions. Just for curiousity's sake, why do you want to convert to PDF? It's a horrible format for ebooks.