Novated Lease reporting under Gross Payments STP1

We were reporting under STP1 to 30 June 2022.  On our EOY Finalisation (MYOB Advanced) the Gross Payments for staff with novated leases was calculated as Total Gross less Pre-Tax component of novated lease - but only for the months Jul-Mar.  When I queried this with our MYOB Partner they explained this was because it was in line with the FBT year, and that the Pre-Tax deductions for Apr-Jun would be included in the next FY EOY Finalisations.  This doesn't seem to make sense.  These staff were taxed on the adjusted gross amounts (after Pre-Tax deductions were applied), but the full Gross Payment is included in their Payment Summaries for the month's Apr-Jun.  This will surely result in them paying extra tax when they lodge their tax returns?  I have tried getting answers from ATO without any luck.