Taxes are calculated based on the pay date of the calculation.  When creating the calculation, the year of the date set for the 'Calculations are for this pay date:' field is used.

The IRS rules are centered around when wages are actually paid (not earned), so any wages paid out in January, regardless of previous year overlap, will use the new years taxes when calculated. In short, the employee isn't receiving any of the money until the new year, thus all income is in the new year and falls under that year's taxes.