I'm starting to work with EGit. I've created an initial repository and I've done some changes and commits to get Version2. Then I came back to the initial version and changed some files and I committed the changes. I did a merge with some conflicts and this is the resulting tree:

The strange thing is that when I checkout from one branch to another some files appear unstaged (">"). To fix this I reset the changes, but when I checkout to another branch it happens again.
If I close Eclipse and I open the repository in Git Extensions I can checkout different branches without any problem.
Sometimes when I want to reset the changes from Eclipse to remove this "ghost changes" I can't do it because the conflict dialog is reopen again and again when I press the reset button.
EDIT: I post the Diff o a file.
diff --git a/MyApp/res/values/styles.xml b/MyApp/res/values/styles.xml
index 79a39af..afe1d34 100644
--- a/MyApp/res/values/styles.xml
+++ b/MyApp/res/values/styles.xml
@@ -1,13 +1,13 @@
 <resources>
     <!--
-        Base application theme, dependent on API level. This theme is replaced
+        Base application theme, dependent on API level. This theme is replaced
         by AppBaseTheme from res/values-vXX/styles.xml on newer devices.
     -->
     <style name="AppBaseTheme" parent="android:Theme.Light">
         <!--
-            Theme customizations available in newer API levels can go in
-            res/values-vXX/styles.xml, while customizations related to
+            Theme customizations available in newer API levels can go in
+            res/values-vXX/styles.xml, while customizations related to
             backward-compatibility can go here.
         -->
     </style>
It's seems that the differences are when there is a CRLF.
 
     
    