Do you have Mail set to delete messages after a specific period of time? This is a per-account setting, so you need to check it for all accounts. Also, Gmail's IMAP implementation is _very_ nonstandard so if you're using Gmail, it may not work.
As an aside, I'll note that there are MANY issues with archiving sent mails. While email is "standardized," unsent email is not and there are no good headers on sent mail messages. I would actually recommend that if you need to rely on tracking sent mail, that you actually set it so you bcc: yourself on every message you send, and then just have Mail delete your sent mail folder on a daily basis. The bcc; emails you can file away, and they *are* stamped with mail headers, so they're much more reliable for... just about everything.
Take this as helpful advice from someone who has used a LOT of mail clients and seen all the issues involved with said sent mails ;-)