FBT exempt payments for DGR business

We are having trouble getting our payment summaries correct. We are a NFP with PBI status and our employees deduct the standard $611 pre tax to their home loans each pay. The ATO is wanting to charge tax on these payments despite our exemption under S57A. We believe we have the wrong tax status loaded for the employee. We believe that under wages and under deductions both FBT exempt categories should show as not reportable. This does not seem to fix the problem. We have had no luck speaking with MYOB and no luck with the ATO. I need assistance urgently. Chris