After bisecting this problem I ended up with the mentioned commit that 
completely breaks git-svn for me on Windows (mingw/msys version).

#> git svn rebase
warning: unable to access '': Invalid argument
warning: unable to access '': Invalid argument
fatal: unable to access '../../../../w:/work/my/repo.git/.git/config': Invalid 
fatal: index file open failed: Invalid argument
Cannot rebase: You have unstaged changes.
Please commit or stash them.
rebase refs/remotes/trunk: command returned error: 1

Please note that I use the official git repository as-is, this one (no 
additional patches):

e02ca72f70ed8f0268a81f72cb3230c72e538e77 is the first bad commit
commit e02ca72f70ed8f0268a81f72cb3230c72e538e77
Author: Jiang Xin
Date:   Tue Jun 25 23:53:43 2013 +0800

    path.c: refactor relative_path(), not only strip prefix

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