I have the same issue, just installed fresh copy of Sabayon 5.0 Gnome x86_64, it checked for updates, has found 800 updated packages, but is failing to update anything claiming that it can't find libvdpau-0.3-r1. The same thing with equo, it says that the libvdpau-0.3-r1 package is probably needed by nvidia driver package. I can't update/install anything except with emerge. Besides, Nautilus was buggy, I couldn't enter its Edit -> Preferences because it was crashing, I found the same problem and the solution (to reinstall it using emerge) in this forum, did it, now I can use Preferences, but, surprise-surprise, when I want to see the properties of any file with right-click -> Properties, Nautilus crashes. Sad.
Anyway, dear developers, thank you for your hard work, I hope I can fix these problems with your help.