It seems that the ./scripts/repository/reconcile.php script doesn't use the SSH credentials that were configured for the repository.
> ./scripts/repository/reconcile.php X Loading commits... Updating repository.. Unable to `git fetch` the working copy to update it. Reconciliation requires an up-to-date working copy. [2014-04-10 08:02:50] EXCEPTION: (CommandException) Command failed with error #1! COMMAND git fetch --all STDOUT Fetching origin STDERR Permission denied (publickey). fatal: The remote end hung up unexpectedly error: Could not fetch origin at [/data/www/libphutil/src/future/exec/ExecFuture.php:398] #0 ExecFuture::resolvex() called at [/data/www/phabricator/src/applications/repository/storage/PhabricatorRepository.php:291] #1 PhabricatorRepository::execxLocalCommand(fetch --all) called at [/data/www/phabricator/scripts/repository/reconcile.php:65]