But there still quite a difference between claiming that 1/3 or 2/3 of randomized studies are wrong.

Yes, the 2/3 is probably an error on Eliezer's part. He doesn't say randomized, so he could be misremembering the 5/6, but the 5/6 is probably not the figure to quote and Ioannidis is a little misleading in putting it first. Only 6 of the 45 highly-cited studies were retrospective and I think that is representative of medical research in the prestigious journals. (the discussion of the control group should address this, but I don't see it)