I have the same problem (running Wubi with Ubuntu 12.04) and it's
rendering my computer virtually unusable. I have also had this problem
on a different computer running Wubi with Ubuntu 11.10. I have been
using Wubi with Ubuntu 11.04 on the same machine with no problems in the
past. All have been clean installs (i.e. not upgraded from previous
versions). My version of ntfs-3g is "ntfs-3g 2012.1.15AR.5 integrated
FUSE 27" (though the problem has existed for other versions after Ubuntu
11.04).

mount.ntfs appears to run whenever write-to-hard-drive is occurring.
Additionally, it blocks most applications from running (presumably as
they all eventually need to read/write to HDD), resulting in greying out
of the application window for a few minutes. It's especially problematic
when doing >1MB file operations (e.g. installing packages with apt-get).
The Windows install is barely used, so it's unlikely to be highly
fragmented.

I have tried various things mentioned in this thread to no effect (I
came unstuck with the suggestion to backport ntfs-3g as Ubuntu refused
to backport fuse/fuse-utils for some reason). I agree that it's bizarre
that this bug has persisted for so long without a fix, especially since
(in my experience) it make Wubi unuseable. I suspect that my solution
will eventually be to give up on Wubi and create a new partition for
Ubuntu, but it's frustrating that I'd have to do this when previous
versions have worked fine.

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https://bugs.launchpad.net/bugs/392204

Title:
  Huge CPU usage by mount.ntfs process

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