Update:
Found the following resource:
https://help.myob.com/wiki/display/myob/Reportable+fringe+benefits+amounts+%28RFBA%29+with+Single+Touch+Payroll+reporting#expand-HowdoIenterreportablebenefitscoveredbySection57AoftheFBTAA1986
This indicates that amounts <$3773 do not need to be reported.
When I removed all the smaller amounts and left only the >$3773 amounts, the submission to the ATO was approved for RFBA affected staff.
Finalization of all other employee pays were submitted as a second batch (with unchanged figures).
It appears that the problem is solved.
