The SQL Clone Agent Installer has a built-in timeout when trying to start during the installation process. The error doesn't always mean there has been a problem with installing the agent only that it is taking longer than we expect to start.
To verify if the agent is working after receiving this error open services.msc and verify if the SQL Clone Agent service is started. If so, navigate to http://<CLONESERVERMACHINE>:14145/settings/agents to see the status of the new agent. If this has a green dot everything should be up and running.
In any other circumstance please log a ticket with Support with your log files which can be found in C:\Users\usernameRunningCloneAgentService\AppData\Local\Red Gate\Logs\SQL Clone\Agent x.x.x