I can confirm the issue is still present in the Alpha2 release of natty. I have the same setup as Kent Baxley:

1.) Ubuntu 11.04 alpha2 amd64
2.) USB startup-ISO generated by multisystem
3.) Installation crashes with an Ubiquity assertion error about 75% through installation.

snippet from syslog:

Feb  4 20:29:14 ubuntu plugininstall.py: log-output -t ubiquity chroot /target dpkg-divert --package ubiquity --rename --quiet --remove /usr/sbin/update-initramfs
Feb  4 20:29:14 ubuntu ubiquity: update-initramfs: Generating /boot/initrd.img-2.6.38-1-generic
Feb  4 20:29:14 ubuntu ubiquity: Cannot find /lib/modules/2.6.38-1-generic
Feb  4 20:29:14 ubuntu ubiquity: update-initramfs: failed for /boot/initrd.img-2.6.38-1-generic
Feb  4 20:29:14 ubuntu plugininstall.py: log-output -t ubiquity chroot /target update-initramfs -c -k 2.6.38-1-generic
Feb  4 20:29:14 ubuntu plugininstall.py: log-output -t ubiquity umount /target/tmp/.X11-unix
Feb  4 20:29:14 ubuntu plugininstall.py: log-output -t ubiquity chroot /target umount /sys
Feb  4 20:29:14 ubuntu plugininstall.py: log-output -t ubiquity chroot /target umount /proc
Feb  4 20:29:14 ubuntu plugininstall.py: log-output -t ubiquity umount /target/dev
Feb  4 20:29:14 ubuntu plugininstall.py: log-output -t ubiquity chroot /target mount -t proc proc /proc
Feb  4 20:29:15 ubuntu plugininstall.py: log-output -t ubiquity chroot /target mount -t sysfs sysfs /sys
Feb  4 20:29:15 ubuntu plugininstall.py: log-output -t ubiquity mount --bind /dev /target/dev
Feb  4 20:29:15 ubuntu plugininstall.py: log-output -t ubiquity chroot /target umount /sys
Feb  4 20:29:15 ubuntu plugininstall.py: log-output -t ubiquity chroot /target umount /proc
Feb  4 20:29:15 ubuntu plugininstall.py: log-output -t ubiquity umount /target/dev
Feb  4 20:29:20 ubuntu ubiquity: umount: /target/cdrom: not mounted
Feb  4 20:29:20 ubuntu plugininstall.py: log-output -t ubiquity umount /target/cdrom
Feb  4 20:29:20 ubuntu finish-install: Disabling CD in sources.list
Feb  4 20:29:20 ubuntu plugininstall.py: Exception during installation:
Feb  4 20:29:20 ubuntu plugininstall.py: Traceback (most recent call last):
Feb  4 20:29:20 ubuntu plugininstall.py:   File "/usr/share/ubiquity/plugininstall.py", line 1440, in <module>
Feb  4 20:29:20 ubuntu plugininstall.py:     install.run()
Feb  4 20:29:20 ubuntu plugininstall.py:   File "/usr/share/ubiquity/plugininstall.py", line 55, in wrapper
Feb  4 20:29:20 ubuntu plugininstall.py:     func(self)
Feb  4 20:29:20 ubuntu plugininstall.py:   File "/usr/share/ubiquity/plugininstall.py", line 174, in run
Feb  4 20:29:20 ubuntu plugininstall.py:     self.install_extras()
Feb  4 20:29:20 ubuntu plugininstall.py:   File "/usr/share/ubiquity/plugininstall.py", line 1029, in install_extras
Feb  4 20:29:20 ubuntu plugininstall.py:     self.do_install([package])
Feb  4 20:29:20 ubuntu plugininstall.py:   File "/usr/lib/ubiquity/ubiquity/install_misc.py", line 716, in do_install
Feb  4 20:29:20 ubuntu plugininstall.py:     mark_install(cache, pkg)
Feb  4 20:29:20 ubuntu plugininstall.py:   File "/usr/lib/ubiquity/ubiquity/install_misc.py", line 489, in mark_install
Feb  4 20:29:20 ubuntu plugininstall.py:     assert cache._depcache.broken_count == 0
Feb  4 20:29:20 ubuntu plugininstall.py: AssertionError