Based on the scenarios provided, it seems to be based around doing an NFC upload to an ESXi host.
Media upload would upload via NFC directly to an ESXi host (VMs go to vCenter), and the guest customization package is also uploaded via NFC to the ESXi host.
In vCloud Director 5.5 with ESXi 5.5, you only need a vCloud Director agent to be installed if you are using vCloud Network Isolation.
So here are a couple questions/thoughts:
1. As a curiosity, has anything happened recently to the ESXi hosts (password change, etc)
2. If you did install the vCloud Agent (say out of habit), can you un-prepare and prepare each host?
3. If the agent was never installed, can we install it as a test?
If you want to know what it looks like on the ESXi host side, you'd have to search the hostd.log files for :
invalidProperty = "url"
There is a few lines before and after this, and you might have to check all hosts to actually find the error state. That's the one log file we'd need to get to evaluate this further.