I think this is a regression in GTK+ 3 where the notebook tabs are massive and full-width. I'm pretty sure you could tweak it in an application-specific CSS file.
The mentioned warning messages are [due to a bug (fix) in GTK+ as well](https://bugzilla.gnome.org/show_bug.cgi?id=773814). The other warnings from menus are due to some weirdness in GdkPixbuf IIRC.