incorrect vat on checkout page

I've read through many of the similar issues, but I'm not sure which fix to apply to overcome my issue.
I've been playing aroung with a £50 gift voucher in the shop. The shop lists prices that include UK vat @20%
Here is the scenario:
The vat appears correct on the shopping cart screen, but is incorrect on the checkout screen

Shopping cart screen

Subtotal (inc. VAT): £47.92
Coupon Discount: - £30.00

Total (inc. VAT): £17.92
VAT Included: £7.99

when you click CHECKOUT

Subtotal (inc. VAT): £47.92
Coupon Discount: - £30.00

Total (inc. VAT): £17.92
VAT Included: £2.99

when you select a shipping method and click NEXT


Subtotal (inc. VAT): £47.92
Shipping and Handling Fee: £8.65
Coupon Discount: - £30.00

Total (inc. VAT): £26.57
VAT Included: £2.99


when you place the order (I didn't pay it with paypal) and view the order on the orders screen you see

SubTotal (inc. VAT): £39.93
VAT Included: £2.99
Shipping and Handling Fee: £8.65
Shipping Tax: £0.00
Coupon Discount: - £30.00
Total: £26.57

looks like the basket and checkout are the same. So is the incorrect values on the confirm screen?

why did the subtotal change from 47.92 to 39.93?

I've identified the problem, now I need help with the solution. The problem is due to the difference between a coupon and a gift voucher. A coupon should reduce the total and the vat should be the vat of the reduced total. A gift voucher should reduce the total but the vat should be of the original amount as the customer is still paying the full amount just that some of it is with a voucher that he's already bought/has been given.

See the example bleow

CART
Subtotal (inc. VAT): £59.90

Total (inc. VAT): £59.90
VAT Included: £9.98


APPLY COUPON

Subtotal (inc. VAT): £59.90
Coupon Discount: - £50.00

Total (inc. VAT): £9.90
VAT Included: £9.98

CLICK CHECKOUT

Subtotal (inc. VAT): £59.90
Coupon Discount: - £50.00

Total (inc. VAT): £9.90
VAT Included: £1.65


Now if this was a coupon that had been given out free, then the VAT amount after checkout of £1.65 is correct. HOWEVER if someone had bought a Gift Voucher then the VAT amount at checkout should be £9.98


The VAT at checkout should still be £9.98, not £1.65