I am guessing that WSUS was rejecting the packages because they weren't signed by a trusted PublisherThat's right. The wsus doesn't trust the file, even if it came from his upstream server, so it reject it.
Interesting thing is that the Id field still shows up orange...This is a normal situation. Replica servers doesn't fill the "UpdateServicesPackages" folder. Only Upstream servers does it. This is why the field is in Orange and not Red. The situation can be normal.