I pay health insurance thru my employer. The amounts on W2 boxes 1,3 and 5 are the same. Shouldn't box 1 have the amount I paid for health insurance deducted from it?

All three boxes would be reduced by the same amount if you paid for your health insurance premiums via a cafeteria plan (sec. 125). 

Cafeteria plans are exempt from Social Security, Medicare and income tax. Therefore, all three boxes would have the same (pre-tax) amount.

http://smallbusiness.chron.com/payroll-deductions-allowed-before-calculating-social-security-tax-615...