Gents,
I'm a technician.
When I use Web Interface (WI) and answer to user in request, my answer will be added to request. Also you will see that you answered to user@company.com (you see field To: user@company.com in the answer)
But if I use email and answer to ServiceDesk's email and user email, I will see in request only answer without To/CC fields. I.e. you can't chek, was this email sent to user.
Can you please keep in the conversation original To/cc fields from email ?