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Ive also recently moved from a html based site to php and will monitor if this gets me more hits, as its a better layout etc hopefully so.
I feel at the moment i get a very low earning per day compared to the number of visitors i get.
Did you use "new" style code versus old code? Code that supports "Managed Ads", versus code that does not?
I don't believe I'm currently seeing a miscount on unique page views, but your change is huge.
I have noticed an earnings boost anytime I regenerate, AND, republish code, (for a couple days anyway). Many refer to this as a "reset". Historically there have been several ways to "reset" accounts and boost earnings, but I digress.