Comment 4 for bug 1668626

I'm not sure if this constitutes a fix or not, but I was able to get GTK applications looking normal again by going into System Settings and changing the theme to Adwaita or Ambience. I don't think there was any theme set (or a different theme not listed)... and it wasn't easy to select a theme since separators were gone and clicking in the right area was more of a guess. Eventually I got it selected though and everything looked correct again.

When using something like gnome-tweak-tool or lxappearance I have 10 or so GTK themes, but in System Settings->Apperance there are only 4 listed. The themes that are not listed here (ones I have installed myself) don't seem to work at all. If I select Arc or Breeze in gnome-tweak-tool the appearance goes back to looking broken. So it seems like its a problem with some themes and being incompatible with 16.10?

For non-Unity DEs I have added /usr/bin/gnome-settings-daemon to the startup process and that seems to have restored the GTK applications there.