Payroll Taxable Income on Paystub is Incorrect

When we first started using payroll, one of the deductions was marked before tax, but was an after tax deduction.  I have looked every where I can think of and I made some changes to the deduction records, but the tax income on the paystub stills comes out incorrect.  I looked at the report that prints the check, but that did not help me, since it pulls data from an empty table.

Any ideas of where I need to look to fix this?