Same issue here as well.
Every email sent from "form[webmaster_email]" email with a "Reply-to" header parameter but for some odd reason, some users reply back to "form[webmaster_email]" instead of "Reply-to" address.
This happens with almost every provider gmail, rocketmail, yahoo, hotmail. But as I mentioned before, only happens maybe 1 out of 100 email sent.
Those emails all have "X-EsetId" parameter in the header section. Could it be Virus softwares remove the "reply-to" parameter without telling the user or any ideas about this ?