Comment 27 for bug 613288

In Windows 7/Vista, if you get the "boot configuration store could not be opened" error when installing with Wubi, try this:

Go to Administrative Tools -> Computer Management -> Disk Management. See if you have a small (100MB or so) partition at the beginning of one of your drives. On mine (an HP) it's called SYSTEM and is 106MB. Right-click on it, select "Change Drive Letter and Paths..." and if it has no drive letter, add one (it doesn't matter what letter) then close everything and try installing with Wubi again.

Once I assigned a drive letter, bcdedit.exe was able to access the boot configuration store and Wubi installed fine.