The problem is that the reward points are rewarded on the value of the product as stored in the products table (now adjusted by specials, discounts and attributes). If anything calculates it differently then the value will not be available to the reward points module- Therefore the points awarded can never be determined.
The only way around this as far as I see would be to add an extension that allows you to calculate the reward points globally when the total is calculated but then you will lose the capability of setting the global redeem on a group or product basis.
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