on the cart page, change the following code:
<input type="hidden" name="amount_<?php echo $eCart1_Index+1; ?>" id="amount_<?php echo $eCart1_Index+1; ?>" value="<?php echo WA_eCart_FormatNumber($eCart1->DisplayInfo("TotalPrice") - (($eCart1->DisplayInfo("Price")/$eCart1->TotalColumn("TotalPrice")) * $eCart1->GetDiscounts()), false, 2) ?>" />
to:
<input type="hidden" name="amount_<?php echo $eCart1_Index+1; ?>" id="amount_<?php echo $eCart1_Index+1; ?>" value="<?php echo WA_eCart_FormatNumber($eCart1->DisplayInfo("truePrice")), false, 2) ?>" />