Modified files coming from v2.6.12 checkout

I'm trying to do a performance test suggested by Catalin. I cloned (what I thought to be) Linus public kernel tree[1] then locally cloned it again and tried to checkout a working directory of v2.6.12:

  $ git-clone [1]
  $ git-clone -l -n linux-2.6 bigmergetest
  $ cd bigmergetest
  $ ls -a
  .       ..      .git
  $ git-update-ref HEAD $(git-rev-parse --verify v2.6.12^{commit})
  $ git-read-tree HEAD
  $ git-checkout-index -u -a
  git-checkout-index: include/linux/netfilter_ipv4/ipt_connmark.h already exists
  ...
  git-checkout-index: net/ipv4/netfilter/ipt_tos.c already exists
  git-checkout-index: net/ipv6/netfilter/ip6t_mark.c already exists

That can't be right. Why do so many files already exist during an empty checkout? git-status is reporting these files as being modified. If I commit these 'modified' files there's actually a rather large delta if I diff v2.6.12 and the new commit.

I've tried this both with git 1.1.4 and 1.2.0. Same result. I've also tried it with both the v2.6.12 tag and the current HEAD. Same result just different files having the problem.

I just looked at the linux-2.6 directory which I cloned from [1]; it appears to have the same problem but on a slightly different set of files than the v.2.6.12 clone:

  $ git-status | grep modified | wc -l
       18

Thoughts? Suggestions of where to start looking for a fault? Does the fault exist between the chair and the keyboard?

[1] http://www.kernel.org/pub/scm/linux/kernel/git/torvalds/linux-2.6.git/