olamy, I still get "issue doesn't exist in JIRA" under 3.0.5, despite setting Thread Executors to 10 and then getting "Success" upon clicking Validate Settings under the Configure System page. A commit message containing a valid JIRA ID does not get annotated on the build page, nor does a comment get added to the JIRA issue.
So, this blocker isn't resolved, even if the actual symptoms are different from what was originally reported. I don't know whether there are additional configuration changes that need to be made in order for this to work, but if there are, I'd also comment that a migration from 3.0.2 to 3.0.5 should really provide working defaults (e.g., for Thread Executors), or at least more explicit warnings that people must manually adjust their configuration (and specify how) after upgrading, or their JIRA annotations/commenting simply won't work.
I'll try fiddling with a few other settings but if I can't get it working will have to downgrade to 3.0.2 again.