Hi,
the percentage is calculated on the fly in the template around lines 391 of
templates/flexible_darkmart/html/com_virtuemart/category/default.php
it uses this if statement
if ((!empty($basePriceWithTax) && $basePriceWithTax != $salesPrice)) {
then the % is appended by JS
the display here ->
http://flexiblewebdesign.com/virtuemart-2-template-darkmart/index.php?option=com_virtuemart&view=category&virtuemart_category_id=18&Itemid=482
has a config as the screen shot - so only one check box different from you - hmmm
can you try unchecking the one box and check if you have those lines above -
if so there should be some JS in the head appending a class FlexiblePercentage
If you need further help we will need a url etc
Cheers