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.”
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
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.
From adminstrator command prompt:
C:\Diskpart> List volume
C:\Diskpart> Select volume 1 (Considering this is 100 MB system partition)
C:\Diskpart> Online volume
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