First off, I love GP – it is so easy to work with! Recently I converted a site from an older theme to GP, and made the site layout and ad sizes/positions the same. One day-one with the GP theme, all was well and CTR was normal. But on day two and every day after, CTR dropped about 90%. I have other sites that did not show any change in CTR during this timeframe, so I don’t think it was a coincidental Adsense thing.
Any idea what I might have missed when I converted the site? I’ve since switched back to my old theme (which is unsupported, my reason for going to GP).