There are several reasons that Super Contributions may be missing from the Super Clearing batch, and the resolution will be dependent on the cause.
If Super is missing from the Super Clearing batch, the first thing to confirm is whether Super was calculated for the employee in the period. To do this, run the Transaction report:
Go to Payroll, Reports, Transactions, Transaction Reports.
Select Payroll Company, Location and Pay Point.
Enter the employee code in From Employee and To Employee to select the employee.
Select the Pay Frequency and Period End Date.
Tick Include Standard Transactions.
Click Preview.
Check if the transaction includes superannuation.
Super isn't on the Transaction Report
If Super isn't on the Transaction Report, then it didn't calculate for the employee. See why Super didn't calculate for common causes.
You will need to complete a Superannuation Adjustment to process any super that wasn't calculated.
Super is on the Transaction Report
If Super is on the Transaction Report, then it did calculate for the employee, and you need to check the Super Fund setup:
Go to Payroll, Maintenance, Superannuation, Fund.
Edit the missing Fund.
Ensure Use Super Clearing is ticked.
Click OK.
Include the missing super in a batch
Once a Super batch has been created, you can't add to it, i.e. it won't pick up a processed super adjustment or corrected fund. Instead, you create a second batch with the missing values. When balancing the Super Clearing to your Payroll Report, you will need to total both batches.