Yes, that is normal. Box 1 is the amount of your pay that is subject to income tax. If you make pre-tax contributions to a 401k, 403b, or similar, that amount will not show in the Box 1 amount, but it will be in the Box 3 and 5 amounts. Why? The income is subject to Social Security tax (Box 3) and Medicare tax (Box 5) but not to income tax (Box 1). Also, if your employer has a Sect. 125 or "cafeteria" benefits plan, the medical insurance premiums that you pay do not show in the Box 1 amount, but do show in Box 3 and Box 5.
