In this particular instance, the Windows User was companydomain\universal. The universal is non-generic in this example. This meant that when running db-tools init-db, the Java environment that PaperCut is developed in returned the following error:
The server.properties file would require the \ to be escaped if this was the correct method of entering the Windows Authentication details. When using Windows Authentication, the username and password is not required.
More specifically, this error is because \u is reserved in Java for escaping Unicode strings.