NetSuite uses the rate as to when the paycheck was created.
Changes to employee's pay rate or contribution must happen just before payroll in which changes are to be effective.
In cases, where schedule pay rate change falls in between pay periods, NetSuite will use the effective pay rate based on the date when the paycheck was processed. Retroactive effect will not take place.
See example for Salary Employee:
Schedule S Employee 4 has 2 Salary Item with Effective and Expiration Date of 3/1/2013 – 3/16/2013 and 3/17/2013 – 3/31/2013. The employee Pay Frequency is set to Twice a Month and the Last Paid Date was 3/15/2013.
After the payroll was calculated as seen in the screen shot, NetSuite uses the effective rate of 4166.67 (100,000/24).
Looking at the Paycheck History, the paycheck was created on 3/14/2013, where the Effective Rate is currently at 4166.67. If the paycheck for period ending 3/15/2013 was process on 3/17/2013, NetSuite will use the Effective date of 6,250.00 (150,000/24).
The same behavior applies to Wage Employees.