Hello,
I'm running Kali Rolling (4.4.0-kali1-686-pae), HD install.
After updating, upgrading and dist-updating my GNOME is pretty messed up - menu bar buttons in terminal are without no gaps, some tabs like Preferences in terminal or Tweak Tools are barely usable due to visual issues. There are no custom themes installed. Please see the attached screenshots - Kali live from USB and Kali after updating.