Hi Jordan 

This is perhaps due to setup

1. Click Employees
2. Click Payroll Settings
3. Click Details
4. Click Leave Categories
5. Click the Leave balance you wish to be added to the Payslip 
6. Ensure the box Hide accruals from pay slips and Hide balances from pay slips and in employee portal are not ticked
7. Ensure Automatically Accrues is ticked 
8. Click Save 

If the the setup was correct then Id recommend reaching out to Keypay for support you can email them at: support@yourpayroll.com.au 

Hope this helps!