Why does Webmaster Tools' Site performance show that my page speed is slow when PageSpeed Insights shows a good score?

The key to understanding why there is a discrepancy between what Google's PageSpeed insights tool (and other online page load time checking tools) tell you, and what the "Site performance" graph in Webmaster Tools (WMT) shows you, arises from the following:

1. Page speed tools don't really focus on how long it takes for a page to load. Rather, they look at how pages are structured and served in comparison to best practices.
2. WMT Site performance, monitors the page load times of your webpages as people browse them.

Site performance in Webmaster tools is a better indication of how fast or slow webpages load (assuming there are sufficient data points), because this shows real world data.

Let's assume that, by accident, one of your background images is very large. This will slow down the load time of any page on which it appears. However, it won't necessarily be flagged in any page speed tests because they can't make a call on which images you should or shouldn't include.

By the same token, it is possible to inadvertently include all sorts of unnecessary code (HTML, CSS, JS) and images that all slow down a webpage without affecting page speed tests.

Javascript in particular may cause problems if it is not loaded asynchronously - although page speed tests are fairly good at isolating scripts that slow down page load time.

If page load times are slow in Webmaster tools then it is important to find out what it causing the page load event to take a long time to fire. Culprits may be things like CSS images in unused aggregated CSS files.