Ubuntu – NTFS partition not clearly unmounted PLEASE HELP

Install ntfs-3g with sudo apt-get install ntfs-3g. Then run the ntfsfix command on your NTFS partition.

For example:

ntfsfix /dev/hda6

ntfsfix v2.0.0 (libntfs 10:0:0)

Usage: ntfsfix [options] device

Attempt to fix an NTFS partition.

-h, --help             Display this help
-V, --version          Display version information

Developers' email address:

linux-ntfs-dev@lists.sf.net Linux NTFS homepage: http://www.linux-ntfs.org

For newer Ubuntus You can use -b and -d option together. -b tries to fix bad clusters and -d to fix dirty states. So the command can be

sudo ntfsfix -b -d /dev/sda6

--help shows them

ntfsfix v2015.3.14AR.1 (libntfs-3g)

Usage: ntfsfix [options] device
    Attempt to fix an NTFS partition.

    -b, --clear-bad-sectors Clear the bad sector list
    -d, --clear-dirty       Clear the volume dirty flag
    -h, --help              Display this help
    -n, --no-action         Do not write anything
    -V, --version           Display version information

I turned on the PC and didn't realize it didn't have the Ubuntu CD in so it tried to boot into Windows. When I came back to it I realized it had started running chkdsk, because before I couldn't boot into safe mode I scheduled it to run chkdsk. After it completed the Vista partition no longer had an exclamation mark next to it and I am able to shrink it. It's currently shrinking now and its been on the real resize stage for a while but apparently it's normal if it takes a long time. (Extra info: I did cancel it because I didn't think anything was happening but it messed up the partition. Somehow chkdsk was scheduled again so I was able to resize it again. I'll be sure not to cancel it this time.)

So if anyone else has this problem, run chkdsk /r at Safe Mode with Command Prompt, or the recovery console if you have it (I don't).