Keep VERY accurate records of not only what the PPC shows you as results in your reports, but what your logs are showing you. This is a start.
After this, you'll spend most of your time trolling through your logs trying to follow actual traffic from your PPC.
You might want to redirect that PPC traffic "through" a specific page or tag it with your own tracking tag to be sure where it's going.
My log files and Adsense reports never agree on how many page views I show each day. Adsense is always lower than my log files (go figure...LOL)
I know, though, that a certain amount of difference is to be expected between tracking programs. There's no set "difference" to look for, but over time you can build a solid picture f your own "difference" trend - if THAT trend starts rising, I'd suspect issues.
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