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).

>![enter image description here][1]

>![enter image description here][2]

And the CDN is showing the correct favicon as well.

>![enter image description here][3]

Given you and [ChrisF's][4] 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][5].

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. 

  [1]: https://i.sstatic.net/l1SFN.png
  [2]: https://i.sstatic.net/zqZlu.png
  [3]: https://i.sstatic.net/sAGPs.png
  [4]: https://meta.stackexchange.com/questions/256544/chemistry-icon-doesnt-appear-on-realtime-network-questions/256567#comment836670_256544
  [5]: https://meta.stackexchange.com/questions/256544/chemistry-icon-doesnt-appear-on-realtime-network-questions/256567#comment836788_256567