why git-reset needed after "cp -a" of a git repo?

Apologies if this had been discussed before: I wasn't able to find this in
the ML archives.

Sometimes I copy a whole git archive using cp -a, for experimental reasons,
or otherwise; sometimes I rsync several git repos between remote and local
computers to make access faster (it's often faster to rsync two git repos
than to re-clone or deal with merge conflicts).

However, I noticed that after I copy a git repo (using v1.5.2.2), the index
entries are all out of sync, and I need to run git-reset.  Why?  What's in
the index file that changes after a cp -a or rsync that git depends on?  Is
it atime's and if so, aren't they copied by cp -a or rsync?  If it depends
on atime's, what happens if I mount my filesystem with noatime?  Or does
git's index depends on inode numbers which change after a cp -a?  (BTW, I
tried a variety of rsync options and none helped.)  I also briefly looked at
the source code and wasn't able to find the answer.

So, is there a way to efficiently copy a git repo on a local or remote host
w/o having to rerun git-reset afterwards?

Thanks,
Erez.