Why Same Files show up with different Statuses in Git?

First, some background. I have one hard disk separated into two
partitions: one for the version of Windows 7 that shipped on this
rather new Thinkpad (Windows 7 Professional SP1), the other for Fedora
17 (which I installed and keep up-to-date). Of course, it is rather
easy to access the Windows partition from the F17 partition, which I
have been doing with no noticeable problems: the File Explorer
equivalent, Dolphin (the KDE equivalent) will automount the Windows
partition as a filesystem under /media, I only have to enter the
password for 'su'.

I don't think it makes a difference, but for completeness I provide
the options with which I find it mounted:

/dev/sda2 on /media/Windows7_OS type fuseblk
(rw,nosuid,nodev,relatime,user_id=0,group_id=0,default_permissions,allow_other,blksize=4096).

Anyway, the problem is this: the very same files, e.g.
/media/Windows7_OS/cygwin/home/Matthew
Johnson/MrEd/mr.ed/lesson1/images/home-icon.jpg show up as 'modified'
when I type "git status" (in the mr.ed/ dir) using the F17 git client,
but do not show up at all when I type "git status" under the Cygwin
client. This problem is not on all files, only a few, predominantly in
two directories.

Under Windows (cygwin) "git status" shows nothing to commit, only
untracked files, which is what I expect; only under F17 do I get
several modified files -- and these have old dates (e.g. Nov 27).

Yes, that is another important note: I am running Cygwin on the
Windows partition.

The versions of things under the F17 partition are:

  Linux 3.7.3-101.fc17.x86_64 x86_64
  System:  Fedora release 17 (Beefy Miracle)
  KDE:  4.9.5

git --version
git version 1.7.11.7

Under Cygwin, the git version is 1.7.9.

Finally, I did check the git configuration to make sure the same
user.name and user.email are set in both. And in both cases, I made
mr.ed the current directory before executing "git status". Shouldn't
that be enough? Is there anything else that must match in the git
config?