Files copied to NTFS partitions in Ubuntu get deleted by Windows 8

Solution 1:

I found that SSD caching was the cause of the problem, and disabling it solved the issue.

In my case, a program called ExpressCache was handling SSD caching in Windows, and for some reason it doesn't work well with dual boot. I just uninstalled it the normal way you uninstall a program in Windows, and after restart everything was fixed. This however has the disadvantage of giving up the performance boost given by SSD caching. Anyway, I formatted the SSD partition and will now use it as a normal storage drive.

If anyone has a hybrid drive and faced the same problem, first find out what program is handling your SSD caching (It's probably either ExpressCache or Intel RST), then disable SSD caching either from the program options (Intel case) or by uninstalling the program (ExpressCache case).

Until I find an SSD caching software that deals with dual booting, I will stick with this solution.