The amount in Box 4, Social Security tax withheld and the amount in Box 6, Medicare tax withheld are never, ever counted as withholding, (Box 2). They are used to pay your Social Security and Medicare at retirement.
There are sevreral factors that can cause Box es 3 and 5 to be different from your Box 1 wages. A ciommon one is having contributed to a retirment plan. In this case you are taxed on your Box 1 wages, which would be less than Boxes 3 and 5.
