T3 Payroll taxes not calculating correctly

Hello.

On a semi monthly payroll for 09/15 the payroll taxes on the T3 did not match what calcualted during pre-payroll.  Specifically, when looking at the Payroll Journal the amount of payroll tax does not match what is reported on the Payroll Register.  The employee was not affected by this difference.  The amount on the Journal was posted to the GL.  This issue corrected itself on the 09/30 payroll run.  What could potentially cause the Journal and Payroll Register to show differences, but for the Journal not be out of balance?

Thanks!