I wouldn't be surprised if it was still happening, companies play games like this all the time. It's even more damning that the contract actually contradicts itself!
The only way you could practically get the money would be to go through a labour union like the General Union and Tozen. You could do it yourself by going to the 労働基準局 or something but you'd have to be fluent in Japanese and very patient. However, as it's a monetary issue it'll probably be treated quite seriously (in my experience, anyway).
To be honest, teaching in Japan is becoming less and less attractive every day. People can't afford to pay for lessons in person and Skype lessons are undercutting all the chains but all that's going to happen is they'll find ways to cut corners (like this) until they implode. Berlitz is having trouble recruiting now apparently because they've started running their employees into the ground from the get-go and pay almost the same as a convenience store... and they're one of the better places to work!