Hi Carl
While I can't help with your query I can say that sometimes I notice a few of our large PDFs take a few seconds to open by themselves in the browser or need a page refresh to load correctly.
These forum posts may also help http://moodle.org/mod/forum/discuss.php?d=124983#p547655 and
http://moodle.org/mod/forum/discuss.php?d=98092
Cheers
Teresa