Comment 38 for bug 1090829

@yannbuntu: My issue is the same as yours: the underlying bad EFI/ubuntu directory.

I think I can narrow the cause to grub-efi itself:
 1) I have never booted the pc with Secure boot disabled.
 2) I have never run any third party tools like your boot-repair.
 3) I have never added, changed or renamed anything in the EFI partition.
 4) First installation of 12.10 did produce a normal ubuntu directory,
which allowed the installation (but not Windows) to run.
 5) Second and third attempts at installation failed at the grub part.

And yes, after the ubuntu directory is corrupted, grub-efi will complain about it, along with virtually every other tool attempting to access it.

Repeated runs of dosfsck -r did eventually fix the corruption, by deleting the ubuntu directory.