yeah, since you are modifying the total price, you need another calculation for the item level price.
on the confirm page, there will be a line similar to this:
<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("Price") - (($eCart1->DisplayInfo("Price")/$eCart1->TotalColumn("TotalPrice")) * $eCart1->GetDiscounts()), false, 2) ?>" />
modify that to use the realPrice calculation:
<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("realPrice") - (($eCart1->DisplayInfo("realPrice")/$eCart1->TotalColumn("TotalPrice")) * $eCart1->GetDiscounts()), false, 2) ?>" />