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They were taking orthogonal measurements to see if the pattern would appear over and over. Also it sounds like each successive measurement technique was at a lower level than the previous technique. Sounds pretty thorough. I'd love to see some actual data though.

How would you use the access log to determine if client-side javascript was being executed?

Check if it's even being fetched for a start. Assuming it's not inline.

Browser-cache my friend. You'll need to poll the server on page load (or even better in this case, after you load the ad)

For the page in question, count total hits in the server access log and subtract total hits reported by the Javascript analytics software.

Use a javascript function to poll the server for something.

thanks for coining the word "unconfused"