IIS SMTP Proxy Concatenates Mail bodies of multiple email messages!

On my web server I am using a console application to send email notifications to my clients.
This application sends emails to IIS mail pickup folder to leverage Asynchronous processing. In addition to it, Web users also send emails communications to each other.

From past few weeks, scheduled process all of a sudden is behaving strangely. Many clients have got emails in which email bodies of multiple emails are merged together.
Since there is no code changed, I am flagger busted as to why IIS SMTP proxy is doing this. I have done logging, and found out console application email messages just fine, one email body for each message.