I am not the first, who is running into this problem. In a simple SharePoint Designer Workflow I need to send an E-Mail to several recipients, and put a copy of this mail into a library. So, we first configured incoming E-Mails for this library, and then we build our workflow.
Testing the library worked fine. When we send an E-Mail via Outlook, the mail is stored in the library. But when the workflow sends a mail to the library, the message is stored in the drop-folder, but the OWSTIMER-service removes the message without storing in into the library.
After some investigation I saw, that every mail, which is send by the workflow, contains a line "X-Mailer: Windows SharePoint Services (Version 3)". Without this line, the message is stored in the library. Every message, that contains this line, will be removed.
So, I asked my good friend Google and he gave me a wonderful solution: Dave Nixon has posted it in his blog. He used an event sink in the SMTP-services and a small VB-script to remove the X-Mailer-lines from the messages. So, with this solution, whenever a file is stored in the drop-folder, the event is raised and the script removes the X-Mailer-entry.