I have a few more questions after having read your replies to Anton.

First, I would like to check whether there is a difference from Windows 8 in 
processing the "fast restart mode". Please turn this feature back on, then log 
off Windows (to be ready for a fast restart), boot into Ubuntu and show the 
result of :
sudo head -c 30 'Win/$LogFile' | tail -c 4 | od -t x2

Then please provide information about your storage and SSD cacheing. I have a 
computer on which I had to disable the SSD cacheing, because it is used 
differently by Windows and Linux. I applied the procedure under "Remove fake 
raid" on
http://askubuntu.com/questions/159645/dual-boot-installation-of-ubuntu-12-04-lts-on-hp-ultrabook-envy-4-1002tx
The "sudo lspci -v" output related to your storage controller may also be 
useful.

I interpret the "change tracking features" mentioned by Anton as a
configuration in which your storage is backed up on some external server
(such as a mirror on the cloud).

Finally, for providing a metadata image, better select a partition with the 
smallest number of files, otherwise the image might be too big. You may also 
prefer a partition hosting files whose names are not confidential.
You can built such an image by (replace sdxx by relevant partition id, it must 
not be mounted, and bzip2 would be better than gzip, but it is much slower) :
sudo ntfsclone -mst -O - /dev/sdxx | gzip > sdxx.image.gz
The resulting file is probably too big for being attached to this issue tracker 
or sent by mail. Uploading to a public server may be required.

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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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