Hello; this is unusual. But in this case, restarting the service should have also resolved the error. That will trigger the Agent Update Checker, which does restart the agents. Most likely, a sort of load error happened on the agent; hard to say what without looking at logs. It's almost always an anti-virus or some sort of program locking files at the wrong time. If it keeps happening, it might be worth investigating further.

Error was related to how we had base install Windows Management Framework/Powershell installed. Updating to WMF/Powershell 4 resolved this error. Working through some mistakes in the scripting, but if I can get through it all without any more questions, I'll mark this post as answered.