I'm using KDE, but I also use some GTK applications. When those GTK apps make a call to an external program, they use the preferred applications set for Gnome rather than the ones I've set.
One example is Gimp. From the Help menu, if I select anything from "GIMP Online" it opens the information in the default web browser. In KDE, my default web browser is Mozilla Firefox, but GTK applications open Opera.
Installing the gnome-control-center
package would probably solve the problem, but that introduces a lot of unnecessary dependencies.