@mr_pingu,

matchbox is not running when hildon-desktop is running (check with ps for yourself . What matchbox-remote does is, presumably, to send a standardized message to the window manager (and hildon-desktop is a window manager). I bet if you were running KDE on your N900 matchbox-remote would still work, assuming that KDE (or whatever WM you'd be using) would follow the "standards" (if you can call it a standard anyway).

In short: think of matchbox-remote as a synonym for wm-remote