Comment 111 for bug 477169

Mark, what might happen is that ntfs (not necessarily ext4) could be left in a dirty state with journal items to be committed.

What it means is that if you boot from Windows or a full Ubuntu installation using their default ntfs driver, those drivers will correctly play back the ntfs journal before accessing any file, hence you would not even notice the issue. But when you boot into Wubi, the ntfs driver within grub does not playback the ntfs journal, which might leave some files in an akward state. In particular root.disk. This would also explain why you can access the files once you boot from Ubuntu, but not from grub.

Try this: do a clean wubi install, upgrade so that you get the new initscripts package and shutdown. You should now not be able to boot back into Ubuntu. Try now to boot into Windows, shutdown cleanly, and boot back into Ubuntu. This should work.

Alternatively, after experiencing booting problems in Wubi, try to boot from a live CD/USB and check the ntfs filesystem.

Again, at this stage this is only speculation on my part, but it seems consistent with most observations so far.

Another thing to try: if you installed Wubi onto a partition which is not the boot partition (say D:\ubuntu), see if you have a D:\wubildr and copy it onto C:\wubildr. Then try to boot.

Thanks for your help!