That is pretty odd. I don't do POP anymore, because, well, POP is evil, but are you still checking the pop from the apache as well?
Any idea what the actual pop server is? I suppose it could be a problem on the server side but that seems almost as unlikely as it being a problem on the ppc side.
From my dim remembrance of the POP3 protocol, you have to do a UIDL and then you RETR the ones you want...
http://en.wikipedia.org/wiki/Post_Office_Protocol
So you'd be stuck in the UIDL processing point.
So, could be a bad POP3 server, or you have so many messages the UIDL processing is blowing up due to out of memory issues perhaps?