@Nic Brough [Adaptavist] It turns out it is a bad DN, as you said in your answer.
AD has a bug apparently, where replication "clashes" can cause odd entries to be generated in AD. In this case, we found three offending entries which looked like this:
The carriage return is no mistake. This is pasted straight out of the AD Users and Computers CPL, and the group name includes a CR.
Removing these offending groups made JIRA happy. They could also probably be filtered out as seen in some of the support articles, since they have "CNF:" in common.
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