Working with git now for a few weeks, and trying to move my Visual SourceSafe repositories to git. I am encountering a weird problem. I have set up a small example repo (see the attached zipfile [ATTACH]n77[/ATTACH] ). Containing a single file dixilinkerr.h. There are three versions of this file. v1: Contains a #pragma message line, and a #define CAT_DIXILINK_ERR v2: Edit: the #pragma message line is removed. v3: Edit: the symbol CAT_DIXILINK_ERR is replaced by EXCPCAT_DIXILINK Watching the repository and working directory in the current state: git status: nothing to commit, working directory clean. git log shows 2 commits: v1 and v2. gitk shows 2 commits: The first one in the root commit is v1. But the second one shows different result depending on the chosen view: gitk Patch view: the last commit is a patch from v1 to v3! (So bypassing v2!!) gitk Tree view: the last commit is v2 THIS IS WEIRD! git show HEAD:dixilinkerr.h Shows v2. So the strange thing: v3 is not really in the repository. If you check out the latest version you get v2. v3 is in my working directory. But git does not see any changed files, and the index is empty. Git commit won't add the file. So the file is kindof halfway checked in... I ran into this problem several times when checking in thousands of files using a script. It seems to happen only when the file size of the two last versions of a file are equal but the contents differ. In the above example the v2 and v3 versions of the file have the same size. I am using msysgit version 1.9.0 on Windows 7. Is this a bug or am I missing something?