Form the Riddler, you need to head down to the southernmost room to reach the next level. If that is the entrance with the ID number, have you tried going north after clicking on it? The room you should reach on the third level looks similar to the one on the second, so if you clicked the entrance an even number of times, you may have just ended up on the second level again. If the description stays the same and you really don't move anywhere, then that would be a problem.
