what all things were selected to get update while you run your USP job ?
I think there is a option available like if you wish to update intrinsic properties or so and blah blah option avialable. look around there. You may get solution to your issue.
can you have a quick check for value set against agent status property for the server in question here ?
if you look in the job run log of the USP job (w/ the property update option selected) that ran against this target just prior to the patching job are there any errors for this target ? (look in the log at the server level - a green check in a USP doesn't always indicate the target server was reachable). it's possible that if the server was unreachable when the usp ran the values got cleared or if the role running the usp was not mapped to a local admin on the target that caused an issue.
when you get that particular error during Patch Analysis it means the BSA is unable to communicate to the client server. The Agent service might not be running on target server or the server might be down.
Have you checked any one target server when you get this error?