Curious. Did you change the working directory folder for your launcher for ServerMain?
Try adding this statement to the code right before the error:
String current = new java.io.File( "." ).getCanonicalPath();
And see what folder your program is executing inside.
As a temporary hack, you can try changing the return statement for ServerMain.chooseNetworkMapFile(...) to:
However, this isn't a good long-term solution, since it will break things when you do multiplayer across multiple computers, if the installation folder isn't the same...