Take all the evidence you have to a tax lawyer. If, as Alex suggests, the NVQ inspectors were aiming to penalise the organisations rather than the individuals, and you still have the contract that states 'Full NVQ relief if paid in full by 31 August 2001', then I would think that you have a very good case that it is the school, and not you, that is liable.
I belive your liability is, in any case, to the Inland Revenue, and not to the school. If they have made unauthorised payments on your behalf to the taxman, you may well have a further case against them. Above all, take legal advice before paying anything.