Thanks everyone for your replies.
When I was almost frustrated enough to go through the Tomcat server behind one of the commented out applications, it occurred to me to use a more brute force solution, since the suggestions above didn't seem to work in my case.
In the end I renamed the file system folder and went with the following route:
location ~ /intraStatic/ {
autoindex off;
root e:/fileserver/;
break;
}
Thanks anyway for taking the time to help me find a solution.