Two things come to mind very quickly.

You indicated that historical amounts have been entered but have you turned off history for Payroll. If not then the calculations have to be entered manually.

The other possibility is that there is an icon on the toolbar in the Payroll Journal window that indicates to calculate taxes automatically. This is a toggle switch tied to the icon on its right which calculates taxes manually. Be sure the automatic one is turned on (it will have a box around it)

Hope this solves the problem for you.

But if not, I would then check to be sure all of the settings are set properly "Setup/Settings/Payroll".