I'm experiencing the same issues as in this question: git status shows modifications, git checkout -- <file> doesn't remove them

Git continues to show working directory modifications, even with git config --global core.autocrlf false:

E:\_dev\github\Core [master +0 ~93 -0]> git config --get-all core.autocrlf
false
false

(Note that I've even set the --system setting to be false)

Why does it appear that Git is still modifying my end of lines?

Attempts to get rid of modifications

Baseline

E:\_dev\github\Core [master +0 ~93 -0]> git status
# On branch master
# Changes not staged for commit:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#       modified:   tools/StatLight/StatLight.EULA.txt
... more changes ...
no changes added to commit (use "git add" and/or "git commit -a")

git checkout -- .

E:\_dev\github\Core [master +0 ~93 -0]> git checkout -- .
E:\_dev\github\Core [master +0 ~93 -0]> git status
# On branch master
# Changes not staged for commit:
#   (use "git add <file>..." to update what will be committed) 
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#       modified:   tools/StatLight/StatLight.EULA.txt
... more changes ...
no changes added to commit (use "git add" and/or "git commit -a")

Occasionally this will have an effect in an odd way:

E:\_dev\github\Core [master +0 ~628 -0]> git checkout -- .
E:\_dev\github\Core [master +0 ~361 -0]> git checkout -- .
E:\_dev\github\Core [master +0 ~93 -0]> git checkout -- .
E:\_dev\github\Core [master +0 ~93 -0]> git checkout -- .
E:\_dev\github\Core [master +0 ~93 -0]> git checkout -- .

git reset --hard

E:\_dev\github\Core [master +0 ~93 -0]> git reset --hard
HEAD is now at 11a7f9a Merge pull request #8 from RemiBou/master
E:\_dev\github\Core [master +0 ~93 -0]>

git add .; git stash; git stash drop

E:\_dev\github\Core [master +0 ~93 -0]> git add .
... warnings ....
warning: CRLF will be replaced by LF in tools/StatLight/StatLight.EULA.txt.
The file will have its original line endings in your working directory.

E:\_dev\github\Core [master +0 ~93 -0]> git stash
Saved working directory and index state WIP on master: 11a7f9a Merge pull request #8 from 
RemiBou/master
HEAD is now at 11a7f9a Merge pull request #8 from RemiBou/master

E:\_dev\github\Core [master +0 ~93 -0]> git stash drop
Dropped refs/stash@{0} (de4c3c863dbad789aeaf563b4826b3aa41bf11b7)

E:\_dev\github\Core [master +0 ~93 -0]> git status .\tools\StatLight\StatLight.EULA.txt
# On branch master
# Changes not staged for commit:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#       modified:   tools/StatLight/StatLight.EULA.txt
#
no changes added to commit (use "git add" and/or "git commit -a")

This seems like a bug in msysgit indeed. As a workaround, try creating a .gitattributes file containing

* -text

This will tell git not to perform EOL conversions on any files.