That was it ! I uninstalled ExpressCache and the problem was gone, so
was SSD caching. I tried re-installing it but the problem occurred
again. I think I will have to give up SSD caching :(

Thanks a lot Jean and Anton for your help, I really appreciate it. One
last request, If you know any way to make SSD caching work with dual
booting, please let me know.

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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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