Your tax code is irrelevant. That is simply the amount ( subject to multiplying by 10 ) that you are allowed to earn before tax calculations at the prevailing rates start to apply.
This is the bit that should clear up the question for you. If your allowances are subject to tax on only lets say 30% of the total, then only that amount shows as your earnings in the P60. You then pay tax at your highest marginal rate ( lets say 40% ) on only that amount. As a result the amounts earned and tax paid does tally.
By way of example assume the last £5000 of your salary earned, is taxed at 40 %. For this amount you should have paid higher rate income tax of 40 % that amounts to a tax liability of £2000.
You now want to take into account the £6000 you earned in allowances. Your confusion stems from the fact that only 30 % of that amount is subject to taxation. so the taxman thinks you have a liability of ( £6000 x 40 % = ) £2400. When in fact you know that the liability is (6000x 30% x 40% = ) £ 720.
In fact the amount shown as earned ( from allowances or anything else ) is (6000 x 30% = ) £1800 as opposed to £6000. As a result when the normal taxation calculation is applied then salary plus allowances as adjusted minus applicable tax is correct.
If this doesn't clear it up please e-mail me with your credit card number and I will be happy to go into more depth.
