I found out the hard way that the MSC doesn't care. They won't help you fix with problem with the restaurant, and as long as you don't post a public review there is no reason to tell them. And you CANNOT tell the restaurant manager, or the corporate people that you are a mystery shopper. You don't have to tell them the reason you decided to eat there at all.
Talk to the manager first, show them your copy of the credit card receipt, and whatever proof you have that the server changed it, or added more money to your check. If the manager of the restaurant can't or won't fix it, then you go on the website and file a complaint with the company, again with your proof..
Never reveal that you're the mystery shopper, and never threaten to make a public fuss, like a review. You can threaten filing a complaint with the BBB, but that means nothing if they aren't going to give you back your money.