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I have not used NAVMSE 2.5, but I wonder if perhaps the installation of it somehow disabled POP3 access for existing users. You might check in Active Directory Users and Computers and verify that the POP3 protocol is still enabled for the affected users. If it is, check the POP3 server in Exchange System Manager to see if it has been changed or reconfigured (I don't think it would be disabled because you said new accounts work fine).
You might also try taking a network capture using Network Monitor to see what the actual POP3 return code is. Then, search Microsoft's Knowledge Base and TechNet for details on that code.
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