As you can see the new design is live, which means Physics-SE has been officially launched, and is no longer a Beta site! Congratulations! Also, thank you for the feedback on the design.
I decided not to use the handwritten font as much I did in the mockups. I agree with you that they're a bit harder to read at a smaller size. I'm only using it for the top nav and header text.
If you're still seeing the old favicons, load the follow two urls in your browser and hard refresh:
If you see any CSS glitches, please start a new post, and tag it with "Design" and "Bug" so I can track them easily.
Once again, congrats!