I retested - this issue same with JA Megastore and with protostar too. Problem solved. I copied this file:
public_html/components/com_virtuemart/sublayouts/prices.php to public_html/templates/ja_megastore/html/com_virtuemart/sublayouts/prices.php
and edited
from
//if (round($product->prices['basePrice'],$currency->_priceConfig['basePriceVariant'][1]) != $product->prices['basePriceVariant']) {
echo $currency->createPriceDiv ('basePriceVariant', 'COM_VIRTUEMART_PRODUCT_BASEPRICE_VARIANT', $product->prices);
//}
To
if (round($product->prices['salesPrice'],$currency->_priceConfig['basePriceVariant'][1]) != $product->prices['basePriceVariant']) {
echo $currency->createPriceDiv ('basePriceVariant', 'COM_VIRTUEMART_PRODUCT_BASEPRICE_VARIANT', $product->prices);
}
VM configuration - i enabled:
New baseprice modified by chosen product variant
Final salesprice
Discount amount