I submitted a new Flexible Work Agreement effective mid-pay period and expected my taxes to change on that effective date. Why did they change for my whole paycheck?

For tax purposes, Flexible Work Agreement changes must be effective at the beginning of a biweekly or monthly pay period for biweekly and monthly employees respectively.  If a change is made effective mid-pay period, the tax localities and percentage allocations active at the end of the pay period will apply to the entire pay period.