One of my sites I had to take down the other day due to too much bandwidth being used, well when the site was down I ended up putting up a little "website down" notice, however I also put a Google Ad on their (468*60 Web banner) along with a big-ish announcement about the site being down (so I cannot get targetted for a "non-content" page) and I ended up earning $16 in one day!! Yet when the site is running I'm only getting around $1.5 / $2 a day now. Weird isn't it!!
Sounds like your sites ad placement is wrong, style is wrong, colour is wrong - either, or. Have you tried working it around with different placements and colours?
CTR doesn't mean anything. CTR rate is calculated by: Page Views / Clicks = CTR Therefore as only one page is available, the CTR would obviously show higher than usual, unless every visitor who clicked on previous days did so while browsing through the site, not straight on the homepage.