The sort order of the modules should not affect the outcome of the calculations. Must admit I had that wrong at one time, largely due to the number of encounters I'd had with buggy modules over the years..

That said, I believe that points should be allowed to be awarded for cash purchase amounts only, or the gift voucher COUNTED as cash at the store owners discretion. In short - points should be awarded to the purchaser of the GV, or the person who executes it, but not both.
BTW - this is rather made worse by the mixture of Gift Certificate and Gift Voucher functionality in the same module set.
As I have come to understand it, a GV is a GIFT from the store owner to a customer, and a Gift Certificate is a cash instrument used to pass cash value to a third party.
These two things should REALLY have separate module sets and not share language entries.......
Would make issues like this easier to deal with in the long run....
David