git repository modified after migration

I migrated a 11G git repository converted from svn on a host with Debian 8.2, reiserfs, git 2.1.4 to a host with Ubuntu 12.04.5 LTS, xfs, git 2.6.4. After the migration, `git status` showing a good amount of files modified.

I did the transfer with
1) `rsync -azP`, after noticing the modified files I ran `rsync -avH
--delete` but it did not correct the problem
2) tar zcf, then on the destination download the tar.gz (served by
nginx) with wget

Both had the same result. But the original repository was still clean.

I did some comparison between "modified" and original files a) same hash (md5sum, shasum) b) same permission (-rw-r--r-- 1 ) c) same encoding and line termination (UTF-8 Unicode (with BOM) text, with CRLF line terminators) d) no git attributes for either

On the destination host, I ran `git checkout` on each of those modified files. After one pass I got less modified files. Repeating `git checkout` on remaining files for a few more times, finally I got a clean repository on the destination host.

What could have caused git to consider those files as modified? And why multiple `git checkout` again the same file was necessary?

Thanks.

Yang