I don't know, you don't give enough information, what you've changed, the decrease in ctr, etc. I'm not a medium.
Please post an image of your previous CTR, your current CTR, and your website hits. It could be that you got a load of hits from someone, and now the people coming back are return users so the ads just blend in.
Adsense works best for impulsive clickers so you need to get an ad right at the beginning of content. Top left works best. Once people start reading they stick to the content and hardly every move their eyes away. All those sidebar ads just make your site look nice but they are not effective in earning money.
Get an ad block in the header area, that works the best. To further improve things, add a 336 ad in your content area.
I think most of your visitors dont even see your ads if they click on a link before they scroll down. As RovingCalypso said, make sure they dont have to scroll to see the ads.