Improper W-2 wages are flowing to Section 199A worksheets from the "Wages and Salaries" entries on Forms 1065, 1120S, 8825, etc.  "Wages and Salaries" generally includes pension contributions and other items that are excluded from "W-2 Wages".  Only W-2 Wages are allowed to be used for the Section 199A deduction.  ProSeries needs to have a separate entry for W-2 Wages that will flow through to the Section 199A "Wages" entry.

As a work around, enter only W-2 Wages in the "Wages and Salaries" boxes of Forms 1065, 1120S, 8825, etc., and enter the difference as an "Other Expense" as "Non W-2 wages not reported on line XX" (line XX being the "Wages and Salaries" box).