First of all, this is really strange issue, not something we see from time to time during the deployment.
Secondly, I'm afraid I wasn't clear enough in my last message - you need to check Operations Manager log on the collector service, not on the server, although I would check both, but you've already checked one, so please - make sure you've checked the agent log. Could you also check that you have ID:999 event in this SCOM agent log? If you have it - let us know what's in it.
Also it would help us if you can do "Export Logs" in the nworks UI (Help menu) and send us the bundle it produces, you can send it via direct message in this forum.