I was paid on several occasions at the agreed upon rate. So far only once at the new rate. He also promised the same compensation to the other contractors, and several times while we were all together.
Try talking to him in person and seeing if you can come to an agreement. If so, have an amendment put in place to the contract stating you will be paid the price per student. If you can't come to an agreement, draft a formal letter and send it certified mail letting him know of your disagreement in the changes being made to the payment. If you haven't cashed the check, you could use that as support in your claim that this is not the agreed upon rate.