I've been working for two months now on improving our response time (mainly server side) on a new forum (a brand new product on a technical point of view) we've launched in Germany a few month ago and I'm a lot surprised by the results I get. I monitor our response time using Apache logs and our own implementation of Boomerang beacon.
Using my stats, I can see that our new product responds in about 680 ms where our old product was responding in about 1050 ms. On the other side, Google Webmaster Tool tells us that our pages have an average response time of about 1500 ms today where it was 700 three months ago with our old product.
I've figured that GWT was taking client side metrics into account so I've added some measures on our Boomerang beacon and everything looks just fine. I've also ran some random pages on ySlow and Google's Page Speed and everything looks better than it was before. We event have a 82% on Google's Page Speed tool which is quite cool for a site with some ads in it :)
Lately, we have signed a deal with Akamai to use two of their products : CDN for our static files (we were using another CDN before but it wasn't very effective) and RMA to improve Networks routes. We have also introduced a new aggressive cache mechanism to ensure that most of the pages served to crawlers are cached by our memcache grid. After checking my metrics, it seems that this changes have improved from 650ms to about 500ms, which is good (still not great but it is definitely an improvement). But webmaster tools continues to report an increasing average response time where we see it decreasing in the same time.
Have you ever had the same kind of weird behavior on your sites while doing performance improvements ? Do you have any idea how to monitor the same thing Google does with Site Performance in Google Webmaster Tools so that we could improve our site and constantly check if it is what Google wants ?
Edit 2011/07/26 : Thanks for your answers guys ! Nevertheless, I was not precise enough. The main issue we have is not with the Site Performance page but with the Crawl Stats one for now. We probably found an issue on our side with some very slow pages (around 3000 ms !!) and we are trying to fix them. I'll keep you posted as soon I'll have some infos. Thanks again !