I've seen this happen before too. I've always assumed it's because it's treating the email like a separate request where it simply doesn't even recognize that there is an ID in the subject field. I've seen this happen more commonly when a client will respond from another email account. Not much to go by, but I have seen it before.
I have found the answer. There are actually three places that you need. You can find the settings here.
If you are wanting to introduce users to a helpdesk system that were not
using one then email integration is a quick way to do that. I agree with KaoS -
it certainly degrades the quality of info both in identifying the correct issue
and also with subsequent ticket history and problem resolution. And, as
joel.gibby said, using the web interface for ticket creation and enabling email
updates to existing tickets would be preferred.
How about this setup:
<li> Under Setup>Email>Options, check "Create Ticket Notes From
<li> Under Setup>Email>Incoming Mail Accounts, uncheck
"Enable E-Mail Tickets"
Setup>Ticket>Options>Clients Can Create Tickets Using, check "Web
Interface" and uncheck "E-Mail"