I have the same problem, when i'm converting pdfs. My solution is to convert them with the mobipocketreader in prc format (simple export them to an USB-Stick), and then i convert and send them with calibre to my prs505.
Works perfect for me, also with small and really large pdfs with more than 1500 pages.
**edit**
@Idolse: No, its not a hardware problem, it is a problem with the xml-output generated at conversion from pdf. Conversion from prc works fine.