I forgot to say that when I first ran the ntfsclone command it gave me the 
following error (although I logged into Ubuntu after a restart from Windows):
ntfsclone v2013.1.13AR.1 (libntfs-3g)
NTFS volume version: 3.1
Cluster size       : 4096 bytes
Current volume size: 229999992832 bytes (230000 MB)
Current device size: 230000000000 bytes (230000 MB)
Scanning volume ...
100.00 percent completed
Accounting clusters ...
Cluster accounting failed at 30036592 (0x1ca5270): extra cluster in $Bitmap
Cluster accounting failed at 30063507 (0x1cabb93): extra cluster in $Bitmap
Cluster accounting failed at 32118944 (0x1ea18a0): missing cluster in $Bitmap
Cluster accounting failed at 32225272 (0x1ebb7f8): missing cluster in $Bitmap
Cluster accounting failed at 32229368 (0x1ebc7f8): missing cluster in $Bitmap
Cluster accounting failed at 32233464 (0x1ebd7f8): missing cluster in $Bitmap
Cluster accounting failed at 32241656 (0x1ebf7f8): missing cluster in $Bitmap
Totally 7 cluster accounting mismatches.
ERROR: Filesystem check failed! Windows wasn't shutdown properly or inconsistent
filesystem. Please run chkdsk /f on Windows then reboot it TWICE.

and running chdsk  on Windows as told I got:
C:\Windows\system32>chkdsk /f F:
The type of the file system is NTFS.
Volume label is Work.

Stage 1: Examining basic file system structure ...

  98560 file records processed.

File verification completed.

  4 large file records processed.

  0 bad file records processed.

Stage 2: Examining file name linkage ...

  132348 index entries processed.

Index verification completed.
CHKDSK is scanning unindexed files for reconnect to their original directory.

  2 unindexed files scanned.
Recovering orphaned file test (98552) into directory file 40399.
CHKDSK is recovering remaining unindexed files.

  1 unindexed files recovered.

Stage 3: Examining security descriptors ...
Security descriptor verification completed.

  16895 data files processed.
CHKDSK is verifying Usn Journal...
Usn Journal verification completed.
Correcting errors in the master file table's (MFT) BITMAP attribute.
CHKDSK discovered free space marked as allocated in the volume bitmap.

Windows has made corrections to the file system.
No further action is required.

 224609368 KB total disk space.
 128978408 KB in 81577 files.
     31476 KB in 16897 indexes.
         0 KB in bad sectors.
    171380 KB in use by the system.
     65536 KB occupied by the log file.
  95428104 KB available on disk.

      4096 bytes in each allocation unit.
  56152342 total allocation units on disk.
  23857026 allocation units available on disk.

then I restarted twice and ran the command and it gave me the image I
attached earlier.

Hope this information helps !

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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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