Hmmmmm, this could be a few possible causes. I have a suggestion and a question.

1. You mention that installing 5.3 resolves the issue. This makes me think that the customization script or sysprep method is fine but it is possible the installation order for the Parent VM may be an issue. Meaning that by following proper best practice of the order of install, you solved the issue. I would try the following, uninstall the agent, uninstall VM tools, reinstall VM tools, reinstall 6.1.1 agent and test.
2. I would be very curious, is this a recent or long standing issue? I guess I will make this a double question! You mention network connectivity is verified. I would try restarting the Horizon View agent service and monitor the connection server VDM log for any entry.

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