It sounds like the deduction does not reduce the wages for state taxes. If you review it is the state tax checked on the tax-ability slide of the item?
Box 1 will be impacted either way, as it is the sum of amounts from various tax tracking types (e.g. Compensation, 401k, 403b,...), regardless of tax-ability.
Box 16 is, like most other boxes, based on the actual wages taxed (wage base), which depends on the taxable settings.