One of my websites has had issues with CTR. Before i redesigned it, it had a ctr of 0.7% (that's zero point seven percent). I have always accepted that this low ctr was due to users not being in the buying phase. After the redesign CTR dropped like a rock. It got down to 0.15%. I couldn't figure out what the hell happened and I started trying everything...Finally i found it. I had disqus advertising enabled. Instead of clicking adsense ads, people were clicking the promoted content that disqus provides. Upon turning it off, my CTR went well north of 1%. Go figure.
I dunno, I had disqus advertising enabled last year and this year and my CTR has doubled. But maybe if I get rid of it, it'll go up even more. I'm about to do so anyway, since they're waffling on paying out.