There is an issue affecting customers using HMRC's online filing product to file their 2007/8 Self Assessment tax return if they have requested to have any tax underpaid collected through their PAYE tax code.
If a tax return was filed online before 30 December 2008, an outstanding tax liability for 2007/08 of less than £2,000 can be collected by an adjustment to next year's PAYE code. After this date, this option should be unavailable but it is still shown on HMRC's free online filing product and will be until 31 January.
If customers use this option believing that having their underpayment coded out is still a valid option, HMRC will show any underpayment in their PAYE tax code if contacted by the taxpayer.
After 9 February HMRC will write to customers who have not contacted them to see if they would like to code out their underpayment in this way provided they qualify under the usual rules.
Taxpayers who filed before 30 December 2008 or who use third party software to file their Self Assessment tax returns are not affected by this problem. Full details are available here