I'm using JIRA 4.1.2 and have a JNDI smtp setup very similar to what the JIRA documentation describes:
I've found some other cases that indicate that this issue can be related to setting the SMTP server in JIRA not using an encrypted protocol. Aparently some SMTP servers require encrypted connection.
I know, it doesn't explain why it would work in the new version of JIRA using the same settings, but I think it'd worth a shot.
For this test, you may want to see this documentation. Alternatively, you can add some extra start up parameters to your JVM for encrypted communication during the authentication phase - mail.smtp.starttls.enable.
This parameter is set up during the start up phase. More info about that can be found in Setting properties and options on startup.
I hope this helps.
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