I am using an old version of Jira, 4.3.3. I created a Mail Server and a Service to create issues from email. This was working perfectly until we added second source (monitoring application) to put emails into the account's inbox. I see the emails going to the inbox and getting deleted by JIRA, but there are no issues being created from emails delivered by the 2nd source. The original source is still working fine. Are there any log files or settings to enable logging that I can review? I am at a loss. Please help.
Look for atlassian-jira.log in the logs directory under JIRA "home" (have a look at admin -> system information to get an exact path)
You should find it's saying stuff like "unable to match this email with a JIRA account that has the right to create issues in the project... deleting it"
If there's nothing obvious in there, then head for https://confluence.atlassian.com/display/JIRAKB/Mail+and+Mail+Handlers+Troubleshooting - it's for a more recent version of JIRA, but has not changed that much, and you've already done part of it.
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