non-default Repositories, Repository Groups, and Proxy Connectors disappear when switching Archiva to Windows service

When I set up Archiva on Tomcat, I was launching Tomcat manually via the command prompt. During this time, I set up 2 repositories (1 with a Stage repository), many remote repositories, a repository group, and a proxy connector. Once I was satisfied with my setup, I set the Tomcat instance as a Windows service.

I was surprised to find that the repositories, repository group, and proxy connector I created were missing. Only the default internal and snapshots repositories remained. The default central remote repository remained. The default proxy connector was still present (the one connecting internal to central). No repository groups remained.

I located ${appserver.base} and found data/repositories. Within that subdirectory path, I found my 2 repositories (+ the stage repository for a total of 3 repos).

Suspecting buggery, I created a new managed repository named test. Sure enough, test appeared in the same subdirectory as the 3 repos I created when Archiva was not launched via Tomcat as a Windows service. Archiva could see test, but it could not see the other 3 repos.

I've attached screenshots showing the Archiva ui and Windows Explorer after I created "test".