Gconf, Dconf, Gsettings too many settings storages for Gnome. Although the latest Gnome 3 uses GSettings only, Qt 4.x still relies on Gconf from Gnome 2.x. So changing the icon theme in Gnome 3 doesn't affect Qt apps. What you need is to copy the theme name from Gsettings to GConf via this command:

$ gconftool-2 --type=string --set "/desktop/gnome/interface/icon_theme" `gsettings get org.gnome.desktop.interface icon-theme | tr -d "'"`

and restart the Qt app.