My site is small compared to what you guys are talking about (2-3K pageviews/day) but using Google Analytics I've found that my repeat visitors are about 50% more likely to click my ads than new visitors.
I think it's because some of the new visitors from search engines aren't as well-targeted. For example, I've got a page of desktop background pictures related to my niche, and I get quite a bit of search engine traffic for desktop backgrounds, but it's not niche-specific. The ads on that page relate to my niche, so the CTR isn't great.
Repeat visitors, on the other hand, know what my site is about and are probably interested in the niche (and the ads therein). So it makes sense that they click more often.