One way to cause this problem is to hibernate your Windows and then use Ubuntu to write files to the NTFS partition. The Windows hibernation file then becomes asynchronous with the new data on the NTFS partition.
One way to loosely verify the this particular problem is just to experiment with it.
Or, use data recovery software on the NTFS partition without booting into Windows. (That is to say: boot into Windows; hibernate Windows; boot into Ubuntu; write some files to NTFS; shutdown; remove laptop disk, plug laptop disk into another computer via USB, and then use recovery software.) The software will pick up files that may or may not be connected with the master file table (MFT). Then you can see that files are in fact written to the NTFS partition, but Windows does not "see" them after restoring the state of the system at hibernation time.
chkdsk from Windows on the NTFS partition might reveal problems.
And, aking1012 mentioned sync, which you can do with
sudo sync before rebooting to assure yourself that all file system data was flushed to disk for troubleshooting purposes.
Was this the source of the problem? Success?