As I stated in the OP, we uninstalled the agent from the audit images and removed the LD unique id entries from the registry. That's when these issues started. We are also imaging from an LD 9.6SP1 core, but are still using 9.5SP2 for production, as we are waiting to upgrade ServiceDesk before we upgrade our prod core to 9.6SP1. So we thought it best to remove all remnants of LD from the audit images.
At any rate, it's working now. Not sure what I did, I just recaptured the audit images after removing the rest of the LANDesk-related entries from the registry. No idea if that's what resolved the issue or not.