The superannuation calculation is enabled by clicking on the superable option on the pay item setup. The superannuation calculation in the payrun is done on the dollar amount of superable pay items being paid. If the employee is on unpaid leave, there will be a zero-dollar amount and therefore no superannuation calculation.
There are two options to have a superannuation calculation for unpaid leave:
Enter a manual adjustment to the employee's payrun.
Set up a fixed amount of superannuation contribution for the employee.