Wubi Installer Error: The boot configuration data store could not be opened

Solution 1:

Go to an administrative command prompt and run bcdedit. This will open your BCD store and output the contents. If it fails with the same exception message then your problem is that Windows needs to be told where the BCD store is. i.e. nothing to do with Wubi (which is what I believe).

To open an administrative command prompt click the Windows key, type cmd, then look above, right click on CMD.EXE and select Run as Administrator.

Refer to Issue 3 here for explanation and potential fix: http://support.microsoft.com/kb/2419286

Edit: more information and fix from the Microsoft support site

Symptoms

When you run Bcdedit /enum you get the following error: “The boot configuration data store could not be opened. The system cannot find the file specified.”

Look for the following registry key HKEY_LOCAL_MACHINE\BCD00000000

If we check under HKLM you will not find the key BCD00000000

Cause

If some 3rd party storage Disk or Storage Management software is installed it may bring all the volume without drive letter offline

Generally 100 MB partition is system partition which contains Boot configuration Database and does not have a drive letter assigned.

Resolution

From an administrator command prompt (right-click CMD.EXE and choose Run as Administrator):

C:\>Diskpart
C:\Diskpart> List volume
C:\Diskpart> Select volume 1 (Considering this is 100 MB system partition)
c:\Diskpart> Online volume
C:\Diskpart> exit