I use to lauch from time to time the "Spider Link CheckUrl", and it never gave more than 300 results (my directory has more than 5000 links).
But I had an idea about the possible bug
In my directory, I have links to download a pdf document.
So, I suppose that the links ending with "document.pdf" don't react like "normal" links for html or php pages. And I suppose that the script is stopped by the first ".pdf" link, because I have not seen such links in the 300 first (and last) results.
Dody, have you tested the Spider Link CheckUrl with such links (links to download .pdf, .ppt or .exe documents) ?