There are no special rules that I know of. If the gross pay is $3600 and the imputed income is $1100, and pre-tax items are $500, the withholding should have been calculated on $4200.
Is the social security and medicare withholding correct for that amount? If yes, then the employer may be using the wrong number of allowances for the federal withholding, or maybe they are using the alternate method for people who have not updated their W-4, or the wrong marital status. It might be reasonable o submit a new W-4 and make sure they enter it correctly. If the social security and medicare withholding does not match the net income, there may be other payroll adjustments you aren't seeing on the pay stub, and you may need to talk to your employer. (And remember when doing the calculation, retirement contributions are still subject to SS and medicare tax. Your taxable income for SS and Medicare may be different than your taxable income for federal and state taxes, but you should still be able to match up the numbers.)
