Should I add in PA company contributions to my deferred compensation plan. Add Box #12 codes D and G and subtracted code C(PA Dept of Revenue) Is that correct?

Received a notice from PA Dept. of Revenue that my gross compensation is incorrect.  They contend that I need to add in W2 box #12 codes D and G and subtract code C.  Your software didn't do that.  This takes me from a refund to owing taxes.