I was trying to find the correct package to submit a bug, and it looks like I'm 
in the right place cause I have an extremely similar issue. Upon each boot I 
like to mount my Windows partition. When I do, each time I reboot I seem to get 
the message posted above, stating that it is scheduled for a check and 
instructing to boot in to Windows twice. I have done this multiple times. 
Chkdsk runs, computer restarts, it loads Windows, everything is fine, I go back 
in to Ubuntu (Kubuntu in my case) and it mounts fine. But after the next reset 
the problem comes right back.
So one step at a time that's:

Boot to Ubuntu, mount Windows partition.
Restart, Boot to Ubuntu.
Unable to mount Windows partition.
Restart, Boot to Windows.
ChkDsk, then Restart.
Boot to Windows again.
Restart, Boot to Ubuntu, mount Windows partition.
--and the cycle starts over.

I'm running Ubuntu 10.10 Maverick Meerkat, and it seems to have started upon 
that update.
Originally I had Ubuntu 9.10 installed.
I have no system updates available at this time.
I'm using 32-bit Ubuntu, currently using KDE.

My command to mount the Windows partition is "sudo mount.ntfs-fuse /dev/sda2 
/media/windows" and the output of the error is:
Volume is scheduled for check.
Please boot into Windows TWICE, or use the 'force' option.
NOTE: If you had not scheduled check and last time accessed this volume
using ntfsmount and shutdown system properly, then init scripts in your
distribution are broken. Please report to your distribution developers
(NOT to us!) that init scripts kill ntfsmount or mount.ntfs-fuse during
shutdown instead of proper umount.
Mount failed.

Thank you for your time.

-- 
mount.ntfs-fuse not properly umounting devices?
https://bugs.launchpad.net/bugs/344631
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