Hi dlmad,
Thanks for posting in the Community!
One of the possible reason why PAYG and superannuation is not showing on the pay slip is because the employee's gross earnings did not reach the threshold. The super contribution threshold amount for the month is based on the entire gross earnings of the employee, regardless of whether the earnings are considered to be ordinary time earnings.
For more detailed information, you can check on this article: How is the minimum Super Threshold amount calculated?
Feel free to drop a comment below if you need further assistance. Have a great day!