NGen cannot proceed because Mscorlib.dll does not have a native image

In the Application event log I see hundreds of error messages like the one below:

.NET Runtime Optimization Service (clr_optimization_v4.0.30319_32) - 1>Failed to compile: System, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 . Error code = 0x80131f06, Event id = 1101

In the ngen.log (C:\WINDOWS\Microsoft.NET\Framework\v4.0.30319) I see errors like the following:

Error compiling System, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089: NGen cannot proceed because Mscorlib.dll does not have a native image (Exception from HRESULT: 0x80131F06)

I also get a similar error message if I run the following command at the command prompt:

ngen install system.dll

I managed to pinpoint the reason why the error is thrown: it is because there is invalid information stored at the following registry keys:

[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Fusion\NativeImagesIndex\v4.0.30319_32\index17c]:

NIUsageMask and ILUsageMask

I could reproduce the error on another machine by deleting the index17c.dat file located at C:\WINDOWS\Microsoft.NET\Framework\v4.0.30319. The file is hidden, empty, and its name dictates the registry path mentioned above.

My question is: What could be the root cause for this? (Someone manually altering the values in the registry is out of the question)