Same problem here after 2.6.31-19 kernel upgrade.   At first I had
enduring trouble and great pain booting manually, and I wanted to share
the instructions that worked for my system.

The greatest point of confusion for me was that there were no /dev/sd...
entries listed via "ls /dev" from the grub command prompt.  Despite
this, my manual boot succeeded when I used "root=/dev/sda2". in my
"linux ..." command.  Also, my host (vista) partition was not mounted
properly, so I could not "ls /ubuntu".  Yet despite that I was able to
successfully specify "loop=/ubuntu/disks/root.disk" in my linux command.

System details:
hardware: lenovo r61i laptop (probably not relevant)
host OS: Windows Vista
wubi version: ? (probably not relevant)
ubuntu version: 9.10

Manual boot instructions:
set root=(loop0)
linux /boot/vmlinuz-2.6.31-16-generic root=/dev/sda2 
loop=/ubuntu/disks/root.disk ro
initrd /boot/initrd.img-2.6.31-16-generic
boot

In Ubuntu after manual root:
"sudo update-grub" ("sudo update-grub2" is equivalent?)

Notes:
You may have to change /dev/sda2 to /dev/sda1.  You need to pick the device 
that corresponds to the windows partition that stores your wubi installation. I 
think I simply used "ls" from the grub command prompt and got info that 
suggested I needed to use sda2. (I think the first partition was the windows 
boot partition).

-- 
After 9.10 grub update can not boot into Wubi install
https://bugs.launchpad.net/bugs/477104
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