Assumption: You are operating from ePO2
I would troubleshoot this way:
1.) check the status of the Agent deployment to the unmanaged systems. If ePO is reporting that the deployment is successful?
a.) If no, troubleshoot the deployment
b.) If yes, check the target system and verify that the agent is installed. If installed, bring up the Agent Status Monitor and perform a "collect and send props"
2.) is the target system able to contact the ePO server?
a.) If no, troubleshoot the network
b.) If yes, search the ePO system tree for the target system.
3.) Is the target system now in the ePO system tree?
a.) If no, check that you do not have a duplicate AgentGUID issue.
b.) if yes, rinse and repeat for the rest of the "troubled" IT assets.
Hopefully, this gets you moving towards a solution.