I raised an issue in Jira and haven't heard anything back yet, its probably the one thing holding us up from deploying service desk now.
We have a service desk project setup, with support@ set as the project email address, and no-reply@ as our main smtp address. If you create a issue in Jira, it sends using the project email address, but if one is created using service desk, it sends using the smtp no-reply address.
This is a big issue, and we can't deploy until this works, our users will respond a lot via email, so right now if they respond if won't go to the right email address to get picked up by Jira for that project. I'm hoping this is a small fix and can get into the next release!
Thanks!