Comment 28 for bug 613288

According to http://support.microsoft.com/kb/2419286 :
Problem: “The boot configuration data store could not be opened. The system cannot find the file specified.”
Symptoms
When you run Bcdedit /enum all 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.

Solution
From adminstrator command prompt:
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

This has been confirmed to work here http://ubuntuforums.org/showthread.php?t=1871823

Note the Microsoft solution also mentions the solution Jason Tucker provided in #27 - but I think it's probably better not to have to assign a drive letter to the system boot partition.

I don't think therefore this is caused by Wubi/Ubuntu