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I changed the colors of the ads, and set a four-color rotation, but all of the colors I use are consistent with my site. My goal was to avoid ad blindness by people who visit multiple pages, while still not being "in your face" with the ads. Although I might describe the resulting effect on the CTR as "teensy", I intend to maintain that color scheme.
Experiment until you find a scheme that works for both you and your readers.
Your ads look better now, but there's still a LOT of background noise that makes the eye avoid that location.
Here's my recommendation to you to do as you please...
Get rid of the google banner ad and put back your fast click banner there.
Put a google leaderboard ad above your entire site (left aligned) with a black background. That would mean lowering your logo, etc, a little bit. Give it a single break of line space beneath it and the rest of your content.
It will then stand out and won't look horrible either. I bet you that makes a load of difference in your CTR
That way you won't have to mess with the layout too much....
I don't think the TOS says anything about ads being "hidden" at certain screen resolutions, but if they can't see they can't click so shouldn't be a problem.