There is always a substantial difference reported between the Google speed tool, and other tools, such as Alexa.
I believe that the "funky javascript" is the reason. There has to be SOME reason, and I think you have found it.
The funny thing is that Google reports much slower times, based upon THEIR OWN code - AdSense, AdSense for search, and Google Analytics.
We are told that our load times are slow, but the reason appears to be Google. And "Too many domain lookups" - let's see, one for the page, and 3 for Google. Which Google recommends we REMOVE, to speed up load time! I don't think that all of the departments at Google talk to each other. Obviously, Google does not want us to remove AdSense code, AdSense for Search code, or Google Analytics code.
Also, I can't count the number of times I have looked down at my status bar, only to see "Waiting for ads.doubleclick.whatever".
[edited by: Sally_Stitts at 10:26 pm (utc) on Sep 27, 2010]