As you can see, everything is in its right place. I've got no idea why it won't read the configuration file.
I am using the .bat file to start the server.
/edit
I fixed it. In the .bat file was a space after the bc2. I didn't edit the .bat file, so that must have been a little mistake by whoever uploaded it. I also had to put the instances folder into the bin folder for the server to recognize it.
-serverInstancePath "instances\%instancefolder%"
I wondered how the .exe was supposed to find that folder if it wasn't in the bin folder.
Also the ServerOptions.ini was broken in the link provided in the tutorial, there are spaces before and after the equal signs.