No, payroll does not (and should not) use two different years calculations.
Tax (etc.) calculations used are based on the cheque date – it doesn’t matter when the pay-period begins or ends. So, if the cheque date is in 2007, 2007 rates are used. And if the cheque date is in 2008 then 2008 rates are used.
So, that’s not the reason.
Now, probably one of two things happened to cause the difference:
– The 1st cheque you mentioned was dated in ’07 and the 2nd in ’08 (therefor two different tax year calculations were used.) Unlikely, but a possibility.
– Something in the employee’s setup was changed – like a TD1 amount.
If that doesn’t explain it, then you really need to get into the ‘guts’ of the payroll calculations and it should be fairly easy to discover exactly what happened. Here is what to do:
On the Payrun table, click on the payrun that contains the 1st cheque you mentioned. In the pane below, click on Notes. Now you’ll see a text listing of the payroll processing for all the cheques in that Payrun. Scroll down and find the employee in question. Then look for — Federal Tax Calculation. There you will see the gory details of the tax calculations.
You should copy the text of the calculations into Notepad to make the next comparison step easier – just left-click and sweep down with he mouse to hilight the text you want, then do Edit Copy in the menu bar at the top of the screen. Open Notepad and Edit Paste. (I would copy the entire block for that employee – not just the tax calculations.)
Now, in the Payrun list, click on the Payrun that contains the 2nd cheque. Look through the Notes for the employee in question and examine the tax calculations there. Compare this to what you copied into Notepad and you will have your answer.