We have just had the exact same issue trying to upgrade vSphere 6.0U3 to 6.5. In our case the eam.properties file located at C:\ProgramData\VMware\vCenterServer\cfg\vmware-eam was completely blank. Luckily we had another vSphere server running 6.0U3, so we copied the contents of the eam.properties file from that server and pasted it in to the blank file on the faulty server. There is one URI at the bottom of the file you will need to change to match the hostname of the server. After that the Agent Manager service started OK.