hi ESN Try this
Drop to shell in directory where ITFlow lives.
Run the following commands:
git fetch --all
git reset --hard origin/master
This should match your local files with the current branch and reset. Then updates should work from now on.
Remember do not modify any files manually under ITFlow as it will break updates and you will have to rerun the above commands to reset it. Although you may modify config.php without breaking the updates.