You are right. I don't think it is a .htaccess issue. They changed the way these variables are sent inside the script (GET to POST). See here in action:
http://demo.x-cart.com/demo/search.php
QT should offer some clues on this why they changed this behavior.
As a tip, using a filtering solution you don't need anymore this customization, and it is much more professional than clicking on links.