I see multiple PhutilLockException logs in the daemon log for PhabricatorRepositoryPullLocalDaemon. They look like this:
[2014-08-18 10:23:06] EXCEPTION: (PhutilProxyException) Error while updating the "rOH" repository. {>} (CommandException) Command failed with error #255! COMMAND '/opt/phabricator/phabricator/bin/repository' update -- 'OH' STDOUT (empty) STDERR [2014-08-18 10:23:06] EXCEPTION: (PhutilLockException) global:phabricator:PhabricatorRepositoryManagementUpdateWorkflow:OH at [<phabricator>/src/infrastructure/util/PhabricatorGlobalLock.php:94] #0 PhabricatorGlobalLock::doLock(double) called at [<phutil>/src/filesystem/PhutilLock.php:167] #1 PhutilLock::lock() called at [<phabricator>/src/applications/repository/management/PhabricatorRepositoryManagementUpdateWorkflow.php:74] #2 PhabricatorRepositoryManagementUpdateWorkflow::execute(PhutilArgumentParser) called at [<phutil>/src/parser/argument/PhutilArgumentParser.php:394] #3 PhutilArgumentParser::parseWorkflowsFull(array) called at [<phutil>/src/parser/argument/PhutilArgumentParser.php:290] #4 PhutilArgumentParser::parseWorkflows(array) called at [<phabricator>/scripts/repository/manage_repositories.php:22] at [<phutil>/src/future/exec/ExecFuture.php:397] #0 phlog(PhutilProxyException) called at [<phabricator>/src/applications/repository/daemon/PhabricatorRepositoryPullLocalDaemon.php:335] #1 PhabricatorRepositoryPullLocalDaemon::resolveUpdateFuture(PhabricatorRepository, ExecFuture, integer) called at [<phabricator>/src/applications/repository/daemon/PhabricatorRepositoryPullLocalDaemon.php:198] #2 PhabricatorRepositoryPullLocalDaemon::run() called at [<phutil>/src/daemon/PhutilDaemon.php:91] #3 PhutilDaemon::execute() called at [<phutil>/scripts/daemon/exec/exec_daemon.php:111]
Following @hach-que's suggestion on IRC, I'm opening a task for this.