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The differences in Boxes 1,3, & 5 are indeed related to money that you earned but had amounts taken out to pay for or contribute to benefits that are not taxable. The retuirement amount is most probably to a 401K. The other items may not be pretaxed. This means that the amounts you paid for the medical will be allowed as deductions when you calculate the Schedule A for medical.
My employer told me the reason I had the difference on these lines was because all of these things where pre tax. so should the total for retirement, health,pharmacy and purchase time be the difference between line 1,3,5? because the difference only adds up the total amount of the retirement. I am sorry, I am filing via turbo tax for the first time and I was just wanting to make sure.
If they verified that all the items were pretaxed then yes, the amount in Box 1 should be lower the total amount of all. You cannot change your own W2 so you will be required to get a corrected W2 from your employer.