If you edit the .q-mail file in your home directory you will probably see your mail directory ./Maildir/ twice. Removing one of the lines solved the problem for me. I'm don't no what caused it though..
Is "DO NOT MODIFY THIS FILE!" not sufficiently clear? That file will be regenerated, which is why we put that warning there. When it is regenerated, your problem will reappear.
Please follow-up in bug 735 - we need details in order to track what's causing this.