Can you take a pic of your pay stub and post it here with the personal info blacked out? Something tells me this is just a simple misunderstanding and the money must be accounted for somewhere. If not, this company would be in serious trouble. Are they a major company or a mom and pop?
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Call your Payroll department. You won't be the first to ask them about it. That's way better than quitting and going to anther company for something this simple.