There is an issue with windows service and out agent where we dont get the logs, I am thinking that is the problem. We are working on addressing this but it wont be fixed until SC 4.1.
To troubleshoot you should run agent from command line, dont use service. Simply create a task in windows scheduler to everytime system starts to start the agent. You need to create a .bat script and in that have "C:/path/to/scAgent3.6.0/snapcreator.exe --start-agent 9090 --verbose --debug >C:/tmp/agent_console.out". This should print agent log console info to a logfile. Also make sure in config SC_AGENT_LOG=Y and agent should log under scAgent3.6.0/logs directory.
Another option is simple run agent from console and leave it open "snapcreator.exe --start-agent 9090 --verbose --debug"