Hello,
The iceScrum Server application provides a bundled pre-configured Tomcat, a standard iceScrum configuration and a utility to start, stop and download / update iceScrum.
This built-in solution is here to provide an easy way to install and try iceScrum without the need to dive into technical details. However to is not suitable for most production contexts because you would want to customize the configuration rather than rely on an opinionated one. In you case, starting iceScrum automatically at windows startup is not covered by iceScrum Server.
If you look at the server.log iceScrum Server logs then you will see the command that is executed by iceScrum Server to start Tomcat. It does not just run startup.bat, it also defines environment variables. Defining them system wide (with absolute paths) is mandatory if you run startup.bat from the outside. I cannot guarantee that this would be enough to solve you issue but you can give it a shot.
