It does not matter if the contribution is pre-tax or not. Your federal withholding does not include pre-tax contributions, but Social Security and Medicare does. So, when you did the after-tax contributions, Box 1,3 and 5 would be the same- with pre-tax, Box 1 is less than Box 3 and 5. (You pay the taxes on that income when you retire or remove it from the account- hence "deferred compensation")
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