I had this problem too.
SVN doesn't do any line ending conversion, so files are committed with CRLF line endings intact. If you then use git-svn to put the project into git then the CRLF endings persist across into the git repository, which is not the state git expects to find itself in - the default being to only have unix/linux (LF) line endings checked in.
When you then check out the files on windows, the autocrlf conversion leaves the files intact (as they already have the correct endings for the current platform), however the process that decides whether there is a difference with the checked in files performs the reverse conversion before comparing, resulting in comparing what it thinks is an LF in the checked out file with an unexpected CRLF in the repository.
As far as I can see your choices are:
Footnote: if you choose option #2 then my experience is that some of the ancillary tools (rebase, patch etc) do not cope with CRLF files and you will end up sooner or later with files with a mix of CRLF and LF (inconsistent line endings). I know of no way of getting the best of both.