Thank you for sending us the problematic EML file.
I tested loading the original email into the MailMessage class and actually I was unable to reproduce the problem that you described.
With the code below:
MailMessage mail = new MailMessage ();
the email parses just correctly. The
HasBodyText property is set to 'true' and the Attachments.Count is "1" as it should be (only the pdf was parsed as attachment). I do not see the ATT00001.txt attachment popping is as you described.
Could you please try to download the email with the latest version of Rebex Secure Mail (e.g. 2015R4.1)? If you still experience the issue with the newest version, please send us a code repro so that we are able to reproduce this issue.