hmm i am not so familiar with what gtk version gnome uses but I am pretty sure it uses gtk2
your amule is most likely compiled with gtk1.2, so thats why it does not take the gtk2 theme.
1. you could get a gtk1.2 theme switcher. and change your gtk1.2 theme
2. you could take wxGTK 2.5.3 for example, compile it with gtk2 support, recompile amule against it and there you go with your theme
stefanero