with gnome3, it is known to be in beta ... it is not stable at this time.
Gnome has dropped support for gnome 2, is many deps required to stay current, was discussion about keeping gnome2 as long as possible in sabayon ... is no longer possible.
In this case, is gnome that is turning your world sideways, is not sabayon's fault to go with gnome3.
same thing happened when kde 3.5 went to 4.0, they had a beta program and pushed it down the users throats . We had no choice ... I was mad, upset ... blamed it on the whole world, I switched from kde to gnome for awhile, a few months went by and I went back to kde. I am now happy with kde4.
Same thing is going on with gnome3 right now, many are moving to xfce, lxde, kde ... in a few months gnome will be better.
About the icon and desktop issue after updating, was a bug upstream that effected sabayon, it does happen.
Is a simple fix, open root terminal and
equo install gdk-pixbuf
Sorry you or anyone was affected by it, if you look at the forums and view the active topics, almost everyone was affected by it. But is simple fix, you may have been able to find it if you looked a little harder
About gnome issue, install another de with your current gnome, learn to use it ... wait until gnome is more stable.