Another interesting situation occurred today. I'll try to describe.
A customer e-mailed us with a new problem today. He did this by replying to an old message we had already answered and closed. He also forgot to add a few more questions for which he did the same thing 2 more times.
As you can see, this introduces the problem where when we reply to e-mail (usually by pressing the R key), the 2nd and 3rd messages are easily overlooked because you only reply to the newest message by pressing R (or even when you just scroll down until you see the reply button and click it). We only found out after the customer, slightly annoyed, asked us why we hadn't answered his earlier inquiries that we overlooked his earlier messages.
Yes this is slightly due to the customer being lazy but not missing a customer's e-mail weighs more for us than having to force the customer to send us new issues in a new e-mail. So I hope you can consider or comment on the following possible solution.
Could this be solved by counting the number of in-reply-to message ID's of the message you're replying to and displaying a warning when it has more than one in-reply-to occurrence in the thread? The warning could be similar to the one you see when you try to answer an e-mail that is already assigned to another worker.
Improvement
Open
improve mail handeling/threading to prevent messages from being overlooked (when requesters reply multiple times to an old message)