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There are a couple things you'll want to check. First, check your recipient policies and make sure they are correct. The recipient policies are used to control incoming e-mail messages; if you don't have a recipient policy that includes the recipient's domain, then the message will not be delivered.
Next, check the queues themselves in Exchange System Manager. Expand the SMTP Virtual Server and select the queues. Are there any messages in the queues? If so, this is where the problem lies (e.g., messages are stuck in the queue). If you look at the properties of a queue with stuck messages, it will tell you why the messages are in the queue (e.g., because an MX record could not be found; because the other end terminated the connection, etc.).
When you are using POP3, you're really just pulling down e-mail from a mailbox into a mail client. Have you tried opening the mailbox(es) using a MAPI client like Outlook to see if the e-mail is even in there?
You could also turn on Diagnostics Logging for various Exchange components (e.g., POP3Svc); however, this may be overkill and if you find messages stuck in the queues, then this will not be necessary.
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