What colour are your bm's? I'm just wondering if your bile is able to get through at all.
Also...that milk thistle could be doing excellent things...I have never had 'yellowy grains' before! I think you're getting something unique and like Hypoguy said...you're getting rid of some type of cholesterol crystal. Maybe your stones are breaking up due to the milk thistle?
I wish I could tell you something definitive!
I guess you will just have to flush again and see...in two weeks.