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Unless I am mistaken there is scope on the tax return to enable you to claim repayment of only part of a repayment as opposed to the total. If you do not claim repayment of the full amount then the balance would remain on your self assessment account and would be set off against any other liabilities for later periods.
A check of the online return will let you see it
If you do not reclaim the repayment the sum overpaid will stay on the self assessment and be set off against later duties that are payable.
On looking at your figures I cannot quite work out the logic of your figures. You say that you paid 2 payts on account of £900 making £1,800 but you have overpaid £1,811 thereby suggesting that your tax payments should have been NIl Then you say that you have to pay £1,100 by 31st Janaury 2009. could you perhaps explain why you should not have paid anythign as POAs last year but this year it should be £2,200.
If you do not claim the repayment it will be set off against the POA due on 31st Janaury and then you could subsequently claim repayment of the balance
Shock and Horror I cannot find the opportunity to only claim part of the repayment - contrary to my earlier thoughts. SORRY -
Payments on account usually arise where you have a source of income (e.g. land & property or self employment etc) that cannot be recovered during the tax year and therefore would normally be payable on the 31st January following the year of assessment However the legislation says that you will pay 50% of the liability on the previous 31st January and again another 50% on 31st July based on the previous years tax liability leaving you to pay any balance that arises based on the actual figures in due course.
Having looked at it you could either do what you suggest or leave the repayment so that it will be set off against the next POA and then you could in due course reclaim the amount standing on your SA statement.
I hope this explains my position and please get back if you still have a problem