When you updated AppGameKit to the most recent version, some of the interpreter files would have been changed too. You need to ensure you have replaced your old files (presumably in the root of C, if you followed the guide) with the new files. For this, I simply copy the entire AGK\IDE folder, however if you want to be more precise, Ancient Lady has posted very helpful instructions to do so, here:
http://forum.thegamecreators.com/?m=forum_view&t=198155&b=46 (3rd post from top).
Once you are sure you are comiling with the most recent interpreter files etc, the 2 icon issus should go away...
Good luck...