As your income was more than £100,000 in 2013/14, you lose £1 of the personal allowance (£9,440) for every £2 of "adjusted net income" over £100,000. So, at an income of £118,880, you have no personal allowance left.
Your taxable income is £127,192. The first £32,010 is taxed at 20% (£6,402.00) and the balance of £95,182 is taxed at 40% (£38,072.80) leaving you with gross tax liability of £44,474.80. As £40,290.75 in tax was deducted through the PAYE system, you are left with an underpayment of £4,184.05.
Take a look here
for information on personal allowances and here
for information on "adjusted net income".
The fact that you were given a personal allowance in your tax code does not make the code right. Tax codes are not always correct and need to be checked like any other document which affects one's finances. If you know that your earnings will exceed £100,000 in the next tax year, you might consider having the adjustment to your tax code made in advance of the start of the tax year so as to avoid an underpayment as much as is possible. Its possible HMRC will do that in any event in the light of your 2014 tax return.
I hope this helps but let me know if you have any further questions.