What is the email client and anitvirus software you use?
This is not a virus issue , its your Anitvirus/Anti spam software.As you are using POP3. I too get this but only when receiving emails. I use kaspersky Internet suit 6 and its spamguard engine marks potential spam messages as SPAM. I think there will be some settings in you AV to make changes. As you are using POP3 you beter get youself a free SSL certificate. so that all your outgoing messages can have your SSL certificate.