...the lady there explained the system was 'VERY' computerised and the 'Historic Vehicle Tick box' would not appear on her selection screen until the 1st of April. Went back on the 1st and all went through OK and got a small rebate on the Tax paid in the post a few weeks later.
That was exactly my experience when I did it - see here:
Historic Vehicle Tax Exemption.
In short, you have to do it at a Post Office from the 1st April after the date your vehicle reached 40.