Hi chrisjones-culti, thanks for posting on the Community. In QuickBooks Online Advanced Payroll, the salary sacrifice should show on the pay run and pay slip. 

To troubleshoot, please open the pay run and then exclude and re-include each employee. To do this, click Actions on the employee and then Exclude from pay run. Then, go to Pay run actions and Add employees. 

Note: If you've finalised they pay run, you will need to unlock it first to make changes. Simply click Pay run actions and Unlock to edit. 

If the deductions do not show after this, please contact our team by live messaging or on 0808 234 5337. Here, we'll have the tools available to set up a screenshare where we can take a closer look.