POP3?!?!?! Lol... IMAP for the win! 
It's possible your outlook version did not, has not, or will not receive an update to include the RapidSSL CA server(s). RapidSSL is a big name, so I'm suspecting a similar issue to that with Godaddy SSL certs that are using SHA-2 instad of SHA-1..Basic gist is they may have a newer CA server at RapidSSL that they have not added to all the common trust-stores as-of yet. Your cert may have been signed by the newer server.
I had the same problem, but with Godaddy. in the case of godaddy, they had added their newer CA server to most browsers and other things, but left out Java... resulting in all java programs not trusting (and in some cases refusing to connect) to services, unless you manually added the CA to your trust store (not something you can do easily with a deployed public application).