How does the taxman consistently get my company car tax wrong ? ?

I am part of the PAYE tax scheme at 40% and receive a company car ( Mondeo 2lt tdci and fuel benift for business and private milage ) and the taxman tells me that I have underpaid tax in a previour year. My understanding is that the goverment set the taxation levels then the tax office work out your code then advise you of the coding for that tax year then they fleece you and rob you blind for the year. I can just about put up with that but to then be advised that having been fleeced for the year I have underpaid and will be fleeced further does not seem right!!