When e-mail is first loaded by the Claws client to the local system, it appears to begin with the oldest messages first, at least when using POP3 protocol (may also occur with IMAP servers). If the remote mail server has tens of thousands of messages in the inbox, it can take days for the local inbox to be filled (if it ever completes), mostly with messages that are never going to be read in the Claws client, if they're ever going to be read at all on any client. If the process fails to complete loading, the latest messages are never loaded. Need to be able to specify loading of newest messages first, as they're always more important to see than older messages that have likely already been at least briefly reviewed by sender and subject.
Protocol POP3 is not designed to work that way and you should really delete mails from your POP3 inbox after download. Have a look at http://tools.ietf.org/html/rfc1939#section-8 Futhermore, to implement that a TOP command still have to be issued for every mail in the server, so with tens of thousands of mails you still have to wait a bit for the headers to download.