I know exactly what you are talking about. I had it happen several times last year, and one of my mail accounts here is doing it right now.
Yesterday at 3:43PM PDT that account delivered it's last e-mail via POP3. Even though e-mails kept arriving in the account, and even though Squirrel Mail (web mail - ugh!!!) shows the new e-mail, my POP3 client on my iBook laptop logs in, shakes hands and reports no new e-mail. It has been doing that for the last 16 hours (maybe a hunderd e-mails) since I reported it to DeramHost support.
Just to verify that once again the problem was not in my 'puter, but was at the 'randy' server, I fired up another machine that had not even used it's e-mail client for over a year, started the mail application and had it look for new e-mail at my Dreamhost accounts.
That POP3 client downloaded 1500 e-mails, including over 300 from the POP3 problem account, but it, too saw nothing newer than 3:43PM PST on that account, just as had happened from my laptop.
In the past when this has happened to me (per my Dreamhost Support History) they have seen no problems even though shortly after they poke around and reply e-mail suddenly floods in via POP3...
There only suggestion of a possible problem is that it might be "server load" causing the hang-up. That is HIGHLY doubtful since the machine that hadn't checked that account for over a year was able to rapidly download over 300 e-mails via POP3, but then stopped at the very same last received e-mail as the other machine.
There is a problem, it is at Dreamhost.
Good luck on getting the problem cleared!
So far, I have zero response from support.
P.S. I just started a search through the problems mentioned here in the forum, and have found others where this happens, such as:
One thing that seems to stand out is even though the problem is at the Dreamhost end (since it happens with multiple, unrelated remote clients), it seems to happen to Mac OS X clients.
Maybe that will help the Dreamhost folks to narrow the problem (though they should have spotted that already themselves).