I'm not sure how Gnome works but it uses gdm for a GUI login, right? You might want to look into that or any Xsession files. Sometimes .xinitrc gets cut out of the loop, so to speak. You might be able to add blackbox to a GUI menu or skip gdm and jump right to .xinitrc and blackbox. I had to do something like that with KDE and kdm and blackbox but, as usual, my memory of the details isn't too good. Hope that points you in a useful direction, anyway.
Oh, or you can edit inittab to boot into CLI (runlevel 3) and do startx from there and duck around the whole GUI boot process.