Yip if I could also chime in here. Having the same issue on my site at http://www.travelandstayinsa.co.za . Before the latest GP Premium update, the logo would shrink to a smaller version to be accommodated in the smaller navigation bar.
Now since the update the logo just disappears. If I set to sticky and static it just appends the smaller logo next to the big one.
Also it appears, as Dave mentioned, when I set the Sticky Navigation Effect to either Slide or Fade, but on None, as I had it previously the logo disappears on scrolling. So not a train-smash, just weird.