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No "scientific" tests were done, so it could be any number of earnings variation factors, so I can't say for certain that it was a "penalty".
Could be just a coincidence.
In SERPS or EPC?
I tried the GeoIP targeting but performance of Y went way downhill and I felt bad serving only foreign visitors to G - and they may not have appreciated it either.
I'll periodically switch Y back on now that I have a method to do it in a minute.
serving only foreign visitors to G
That could have skewed the "performance history" that Google keeps for each ad/site. Visitors outside the US may click less on ads that are usually displayed on your site, so Google's algo flagged the ads as "not performing well (anymore)" for your site (because of the lack of US visitors, who might click them more), which may have led to "worse" ads being served when you switched back to AS.
so far ypn epc has been up and down, but lately it's paying a bit better; i get some great ads in my main sector, and some days ypn earnings even match the adsense earnings... the computing sector i'm also in, tho, has been a lousy match for ypn ads.
so ymmv, depending on the sector you are in... i use geoip for ypn, with the foreign traffic going to adsense, but that's only about 10-15% of my overall adsense traffic.
I've noticed on one of my sites that if I switch the high traffic pages (homepage mostly) back and forth from YPN to AS, overall I make more money. I switch about every 3-4 days. I suspect that this somehow resets things (at least in this particular niche) and I get the higher paying ads more often for a couple of days. I've seen it increase by as much as 80% with this tactic.