Due to the pcmanfm call it seems like your LXDE is still from Lenny. I don't see any connection between xbindkeys and xmodmap in this case but I'll try if calling xmodmap or xbindkeys via autostart will make the keyboard work properly even in Squeeze.

I'd still prefer Squeeze over Lenny but since I'm not a version junkie and don't care for multimedia support in ED I might as well try a pure Lenny.

@qole:
Did you take any notes about creating your ED images, ideally a script?
I guess the main step of creating an image via debootstrap is no big hurdle but considering all the little tweaks you applied afterwards like binding directories from Maemo or adding selected packages from Squeeze I think the effort should not be underestimated. Therefore it would be nice to have some template instead of trying to reverse engineer an existing ED image.