I've been with my employer for 6 years and have never had a problem such as this. I also pay my taxes in monthly instalments that is predetermined by the fonctionnaires.
In the US, I've noticed following the instructions on the W-2 to pick your deductions (and set how much of your check is taken in taxes) does not give the correct amount with some employers. I am not sure if its software or just poor accounting. I started just putting 0 and calling it a day.
