> Does this also happen to files on external devices (such as a usb key) ?
No, I copied a file to my USB flash drive and was able to access it in Windows 
and copy it to an NTFS partition.

> A file has also probably been created in "Win/System Volume 
> Information/Chkdsk"..
File attached.

> When you start Ubuntu after having logged off Windows normally, what is the
> output of :
> sudo head -c 30 'Win/$LogFile' | tail -c 4 | od -t x2
> (Replace Win by your actual mount point, keep the quotes or escape the '$')
>
> What does the same command return when you switch to Ubuntu from
> Windows through a "restart" instead of "shut down" ?

The output in both cases is:
0000000 0001 0001
0000004

** Attachment added: "Windows log file"
   
https://bugs.launchpad.net/ubuntu/+source/ntfs-3g/+bug/1280574/+attachment/3982623/+files/Chkdsk20140118214910.log

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https://bugs.launchpad.net/bugs/1280574

Title:
  Files modified on NTFS partition are seen as corrupted files in
  Windows

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