git-gui disagrees with git status

[Bill Winspur <bwinspur@gmail.com>]

Using git version 1.6.0.4

- Created an eclipse wkspace, with a couple of projects in it.
- Created a git repos at the workspace route, using cli.
- Using cli added the two projects to git - at this point git status
shows the following

=====
bwinspur@elm:~/ca.wydv.
workspaces/008-leaning-group/git-lrng-wksp$ git status
# On branch master
#
# Initial commit
#
# Changes to be committed:
#   (use "git rm --cached <file>..." to unstage)
#
#    new file: git.trial.help.bundle/.classpath
        === omitted details from this post ==
#    new file: git.trial.ui.bundle/.classpath
        === omitted details from this post ==
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#    .metadata/
bwinspur@elm:~/ca.wydv.workspaces/008-leaning-group/git-lrng-wksp$
=====

which is what I expected: my project folders are tracked, and
.metadata/ is untracked.

- now I bring up git gui and it shows all the files under .metadata/ as
unstaged changes, which conflicts with git status, and may be due to a
git-gui bug

Regards,

Bill Winspur