git pull --rebase and losing commits

Hi!

I have put my web site under Git control, and am running into some problems.

Whenever I push changes, I go via a bare repository, which then is pulled into a checked out tree in my "public_html" directory. However, some scripts I have does create files directly under the "public_html", and some of them I want to push into the Git history.

I am trying to use --rebase everywhere to get a linear history in the cases where I have pushed changes to the bare repository while there were uncommited changes to the public_html directory.

I have come up with a script that does this (I have removed the uninteresting non-git commands):

  # Commit local changes
  git add path/to/script/output/*
  for file in $(git diff-index --cached --name-only HEAD); do
   havenew=1
  done
  if [ $havenew = 1 ]; then
   git commit --quiet -m 'Automatic' path/to/script/output/*
  fi

  # Update tree (--strategy=ours avoids merge conflicts)
  git pull --rebase --strategy=ours origin master

  # Push rebased local changes
  git push origin master

  # Update all references
  git fetch origin master:remotes/origin/master

However, this seems to lose commits. When I ran it today, it commited an automatic change, and then pulled a tree that did not contain that change, making the changed file just disappear. I had to dig through the reflog to find it:

- This is the auto-commit:
   608b7eda553552841f4a16167c680fc74ed3c55a 
509926edd306bb2f09f563a7cfda800a4f0fdaed Peter Krefting 
<peter@softwolves.pp.se> 1257162580 +0100      commit: Automatisk 
bloggkommentarsuppdatering

- This is the "git pull":
   509926edd306bb2f09f563a7cfda800a4f0fdaed 
9088bd4801a9008fe3fca0d351f97544cee014f1 Peter Krefting 
<peter@softwolves.pp.se> 1257162583 +0100      rebase finished: 
refs/heads/master onto 9088bd4801a9008fe3fca0d351f97544cee014f1

The history of 9088bd... does not contain the rebased version of 509926..., it just went missing.

I guess I am missing something vital here.

  $ git --version
  git version 1.5.6.5