You may have to make a more determined effort to kill off the flukes and other parasites in the liver and the small intestine. Some of have a hard time killing all the flukes and H. Clark wrote that if there are parasites in the bile system you won't be able to completely cleanse the gall system. I also had a tangle of worms in the intestine that seemed to be hindering bile flow.
You may need to figure out why you have so many stones, usually there is an underlying cause, a digestine/intestinal problem that needs to be treated.
It is very likely that if you waited 3 or 6 months before doing another Liver-Flush you would pass more stones as it takes time for them to travel down the bile ducts to the gallbladder.