So apparently, Windows and Ubuntu do not read the same data, which point
at a cache somewhere not synced when shutting down.

Here are a few URL pointing at a tool from Intel to configure a SSD as a cache.
http://www.pugetsystems.com/labs/articles/How-it-Works-Intel-SSD-Caching-148/
http://www.pcworld.com/article/248828/how_to_setup_intel_smart_response_ssd_caching_technology.html
http://download.intel.com/support/chipsets/sb/intel_smart_response_technology_user_guide_3.pdf

Can you use this tool to determine whether a SSD cache has been
configured ? I would recommend not to change the current setting, as I
do not know the consequences on the installed Windows.

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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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