I have set up our active directory with delegated LDAP authentication (first) and JIRA internal directory second. Then when a customer creates an account in a service desk, he cannot log in. I can see that the user is created, but they are not able to log in.
If I switch it around though, they are then able to log in.
My suspicion is that it is trying to authenticate against AD if its set up as the first auth method.
I would take a look at the the file atlassian-jira.log and see if there are any AD issues that are appearing in the logs. The next thing I would do is try testing the AD connector and seeing if it successfully passes and when the last time it synced was. You can find the atlassian-jira.log in your JIRA Home directory.
If all else fails, go ahead and create a support ticket with atlassian so they can take a look at the logs and see if anything pops up.
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