Where you find the "whitelist" ? I can't see this in the transitions.ini, I see only "blacklist"...
echo whitelist = FBReader >> /usr/share/hildon-desktop/transitions.ini
And what about the lock desktop in portait mode ?
gconftool -st bool /apps/osso/hildon-desktop/desktop_orientation_lock true
gconftool -st bool /apps/osso/hildon-desktop/ui_can_rotate false