My employer includes my 401K deductions as part of my gross income for taxes. Last year, this happened as well. I contribute 4 and my employer matches 100%. I ended up paying more taxes because I didn't pay taxes on the pre-tax 401k money through out the year. Should I be deducting this on my 1040? Perhaps in the IRA section?

First its not a good idea to piggyback your question on someone else's. This can lead to confusion. You should start a new thread. So I've moved your question to its own thread.

On your periodic paycheck you should have 2 entries for Total Gross and taxable gross. Your 401K deductions should not be included in the taxable gross. On your W2, the taxable income should not include 401K deductions.

If your employer is including these amounts in your taxable income, then your paystub and W2 is wrong. However, some plans do allow post tax deduction to a 401K. So maybe that's the issue. Talk to your tax preparer, you may need to file amended returns.

Contact your payroll department and get this straightened out.

You MAY be participating in a Roth 401K, which means the employer match IS added to your taxable income.