I am experiencing a similar issue. Sent an email to a contact through the CRM. Received an email back and it was not logged. Used the forward option, which unfortunately includes my signature and makes it difficult to read.
The first forward did not work. Checked for a duplicate assuming he used another email. No duplicate. I did notice that the email he used was the secondary email for the contact. This is problematic as there is no way to know what the contact will do to respond and having the right information, in the right place, when you need it is critical.
Any thoughts? I am going to post with the secondary email group/email not logging as well.