I'm not an expert on thyroid issues so I can't speak to that. It is probably a good thing to stop the stone softening supplements until your diarrhea stops.
I've had the same experience with getting more stones in some flushes than others. Many people here on the Liver Flush Forum s have had the same experience. Don't wait so long between flushes. Keep flushing regularly until you stop passing stones, then flush a few times a year to keep your gallbladder clear.