I am having the same issue. This seems to occur every time we update NCM/NPM. I wrote up a how-to a while ago when we did these upgrades, but I was different from your solution. Previously I would just have to go to the Windows archive server, run services.msc, look for the SolarWinds Job Engine v2 or the SolarWinds Information Service Agents, hit properties and ensure we were using the proper AD service account for the job. Once we verified that it would start working again.
Unfortunately, I am not seeing either one of these agents in the services window (Win 2k8 R2 Standard SP1).
I tried your approach of providing permissions to the NCM server to the archive folder path (providing Full Control, Change and Read access) but I still get the same message in NCM when validating: Invalid config archive directory
Anyone else have a clue?