The software shouldn't "know" that a message's destination address happens to be one of the sender's other accounts.

No, of course not. (And actually, contrary to my evil twin posting up above, it's perfectly possible to send email to the address you're sending from.)

With my real tech support hat on, I second PoppaG - try all the other possible combinations of your email accounts. If mail is disappearing when you send from account A to account B, try sending from account A to account C, then try sending from account C to account B. Mail disappearing is odd, but it would be very, very odd for mail to start disappearing for one specific combination of email accounts.