When the Startup Type of a Carbon server that is configured as a Windows service is set to Manual and when the instance that the WSO2 server is running on restarts, the WSO2 Server will not get restarted along with it.
For the WSO2 server to be restarted when the Windows instance restarts, you need to set Startup Type to Automatic instead as shown below. See attachment below.
To change this setting, go to Control Panel\All Control Panel Items\Administrative Tools\Services and change the type from Manual to Automatic.