There is a pretty interesting thread named MFA warriorship 101 at WebmasterWorld that tries to explain a theory on how MFAs (Made for AdSense) sites get into your Google AdSense ads. The thread creator explains eCPM, how eCPM is calculated in an ad unit, how an MFA can get a high eCPM, how that spreads and how you can try to prevent it.
I believe that the solution sums up the whole explanation listed in the thread.
The way to prevent this happening, in this example, is to reduce the number of ads on the page to two and price the MFA off your site. You could use, say, a vertical banner instead of the skyscraper and putting it in a hotspot to keep the CTR high.
Eg: if you maintain an overall 8% on the page, the top ad might have a CTR of 5% and the bottom one 3%, giving eCPMs of $25 and $15. This puts the price of the ad slots out of reach of the MFAs.
Forum discussion at WebmasterWorld.