Must be a localized issue as I have no issue seeing it on the Stack Exchange question list and on the hot question side-bar.
In fact, I first noticed the new favicon on the hot question side-bar before I even saw this question (about 12:30 UTC today).
And the CDN is showing the correct favicon as well.
Given you and ChrisF's respective profiles identify you as residents of the United Kingdom, that seems to fit with the idea of a localized issue. I am in the northeast United States and it works for me. Via proxy, you, in fact, confirmed that it was working in other regions.
I know it has been 2 days since the new design went public, but I would wait it out a little longer. Obviously the update has reached some people, but it might just be slow in propagating.