The genext2fs upload I am preparing fixes the permission problems. It is current upstream cvs which is similar to what the upcoming 1.4 release will be.
The new version uses a new device table format. It looks to me like debian-installer does not use the device table (instead it uses mknod/devfs). The new version also changes some options that I believe are not used by d-i ( -D replaces the old -f, and -I replaces the old -i). That is just a head's up in case there are genext2fs invocations outside of debian-installer/installer/build/Makefile that are affected by this change.
