The problem could be related to one or more issues as below:
1. Start of service: Check how the start of service is configured. Features like ENTRY may be used or a date type. If still you have a problem, you could debug how the service period is calculated.
2. Termination model: The payment rules depend on the termination model which depends on term'n reason (in IT 0). In SPRO, under payroll for Australia, there is a folder for Terminations. This folder has a number of steps to be configured. Check which model and set of config are applicable for the particular case in this issue.
If necessary you'd be able to use a user exit or ABAP Enhancement to vary the processing.