I have read that MSM is acidic and can make body acidic. So I was wondering were you doing any kind of alkalizing while on MSM protocol.
I alakalise every morning and before bedtime, by drinking a mix of ACV+baking soda..OR lemon+ baking soda. This should be done on an empty stomach.
I also take Buffered Vitamin C ( Sodium Ascorbate). I never take Ascorbic Acid. I always try to neutralise Ascorbic Acid with Baking Soda before I take it.
Perhaps this is the reason, MSM is not giving me any grief (so far) . I like ACV/lemons because it has potassium as well. But I always neutralise the acid with Baking Soda. Give it try.