Emails from a server will use JIRA or Local timezones (semi unpredictably), never user configured timezones.

Steps to reproduce:

1. Configure your user to use non JIRA default timezones. In my test I used America - GMT -8 Los Angelas.
2. Configure JIRA to auto detect system time.
3. Enable notify me on my changes in the user profile
4. Enable email notifications on a project
5. Configure an outbound email server
6. Create an issue, and verify that the time in the email is correct.
7. Shut down the instance.
8. Change the timezone on instance host. In my case, I used GMT-6 Chicago.
9. Bring the instance back online.
10. Create an issue and see the time. Time will be matched to LOCAL AND JIRA. IGNORES USER SETTING
11. Change JIRA to use GMT-8 Los Angelas.
12. Create an issue and see the email. Time will be matched to JIRA. IGNORES LOCAL TIME AND USER TIME, ONLY VIEWS JIRA TIME
13. Change JIRA time to GMT -6 Chicago.
14. Shut down JIRA.
15. Change local time to GMT -8.
16. Start JIRA.
17. Create an issue. Time will be matched to LOCAL. IGNORES JIRA TIME AND USER TIME, ONLY VIEWS LOCAL TIME