Cygwin Git thinks files are changed when they aren't

[Chloe <starrychloe@oliveyou.net>]

Cygwin Git always thinks files are changed even when they aren't. After 
a commit with a Windows Git, Cygwin Git shows files as modified.

Windows Git
--------------------------
C:\Users\Chloe\workspace\AffiliateArbitrage>git status
On branch master
nothing to commit, working directory clean

C:\Users\Chloe\workspace\AffiliateArbitrage>git --version
git version 1.9.5.msysgit.1
-------------------------

Cygwin Git
-------------------------
$ 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:   .project
         ... dozens of files ....

$ git --version
git version 2.1.4

$ git diff .project
diff --git a/.project b/.project
old mode 100644
new mode 100755


$ ls -l .project
-rwxrwx---+ 1 Chloe None 574 Mar 10 21:28 .project


$ uname -a
CYGWIN_NT-6.3-WOW xps 1.7.35(0.287/5/3) 2015-03-04 12:07 i686 Cygwin

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