EOFY STP 2 reports

I have run all my reports for STP2 to finalise the payroll year to ensure all amounts in MYOB agree witht the STP2 reports.

Even though all figures were correct I have noticed that for a number of employees the Gross YTD figure on the STP EOFY  finalisation page was different to their summary of payment.  And also the Gross YTD total on that page was diffenent to the verification report.   The finalisation page was not showing any OT paid to these particular employees, yet the OT was on the summary of payment.

I noticed these employees were the employees I had terminated in my AccountRight file.  But not yet terminated in STP2.  As we employee casuals and some return during the year I don't do the ATO termination until I am sure they are not returning.  I terminate them in my file so that they don't show up each time I do a pay run.

I returned to my MYOB file and deleted the termination date and did a send update event. 

That fixed the incorrect amounts and now all figures are correct.

Why did this happen and what would be the correct way to terminate employees in my file so they don't keep showing up in pay runs.  Was this a clitch in the system?

I have been on hold for about 2 hours to hopefully discuss this but in the mean time can anyone advise on this issue before I finalise my payroll