**Edited** Update to this was; as a result of the help David Winch gave me in finding a true expert in this area of the law, the CPS ended up dropping all charges against both me and my company. David I cannot thank you enough. PM me your address and I will send you something to warm your cockles in these cold, dank nights. I should also say thanks to Paul who it seems highlighted David to my plight.
To anyone else finding themselves in a similar VAT deposit plight, the only advice I can give is to not simply assume your accountant or book keeper has it in hand, for when the smelly stuff hits the fan it'll only be you in the dock. And if charges do get filed against you, I highly recommend you seeking specialist legal help, this is not a job for your local general solicitor.
Oh, and it was also accepted by the CPS that I hadn't, in fact, been a negligent Director.