How much MSM are you taking? And are you taking vitamin c and vitamin d with it? If you are, you might feel better by taking more. If not, you should start.
MSM forces toxins out of cells and vitamin c neutralizes those toxins. MSM also puts down a protective coating on the mucosal layer in your intestines. Plus has a whole bunch of synergistic actions. You might be shedding the old layer. I had the same type of stools for about 6 weeks after starting MSM... they only stopped looking like that and became normal about 2 weeks ago.