For those who are having issue with transport agent can enable pipeline tracing log. This tracing will capture OR snapshot email message for each agent. So, the basic idea is we can trace what are the changes made by each agent and got an idea where are the culprit coming from.
Below is the step to enable pipeline tracing :
1) Configure sender email address
Set-TransportServer <server> -PipelineTracingSenderAddress <sender_email_address>
2) Configure log location
Set-TransportServer <server> -PipelineTracingPath <log_location>
3) Enable Pipeline Tracing
Set-TransportServer <server> -PipelineTracingEnabled $True
This function was very useful while troubleshoot on the strange behavior like garbage character in email, content missing and etc. Once the message capture, we can see the original message and can simulate back in the lab for further troubleshooting.
Using Pipeline Tracing to Diagnose Transport Agent Problems (http://technet.microsoft.com/en-us/library/bb125198%28v=exchg.80%29.aspx)
How to Enable Pipeline Tracing (http://technet.microsoft.com/en-us/library/bb125018(v=exchg.80).aspx)