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I have tried a few things since this, and nothing has worked so far.
I have also found that AD credentials stop working after the initial discovery of a controller. If you manage the controller credentials after discovering a device, it disregards the domain you've entered. The audit log on the devices displays:
Tue Sep 17 11:07:28 BST [N5600-A: HTTPPool02:debug]: scom_sa:AUTH:error:Login failed for user scom_sa from IP x.x.x.x. reason "User not authenticated"