donde, my limited understanding of the vat issue is this:-
a) if any vehicle (passenger or commercial) has the log book in a company name then vat is deducted from the repair chq but made payable to the company - not the garage, company receiving the chq then pay for repairs including vat, get a vat invoice and claim the vat back.
b)If the log book is in an individuals name and the vehicle is a passenger vehicle then repair chq is paid including vat.
c)If the vehicle is solely commercial, (hiace, pajero etc. coming with no rear seats) and the individual is registered for vat then vat is deducted from the repair chq.
If you fall into category b as outlined above then you should contact the person who dealt with your claim to get the difference issued to you.