There was a report written by Kayla Daniel, supposedly exposing a lot of scandal relating to the Green Pasture cod liver oil. Taken at face value, it was quite damning. But on closer examination, most of it didn't hold up.
I think it's true that the fermentation doesn't agree with everybody and that some people do better on a non fermented oil. But for those it agrees with, the fermented does appear to be more effective.
We addressed some of the concerns here: http://www.naturefoods.co.nz/cod-report