Running Apache 2.4 and PHP-FPM 5.4.16, I noticed that the option
upload_tmp_dir was ignored when executing PHP code.
phpinfo() shows the correct setting, but for instance
sys_get_temp_dir() falls back to the OS' environment setting for the temporary directories as if it weren't set.
To fix this, I had to append a few more lines of config to my PHP-FPM's pool's configuration:
php_admin_value[open_basedir] = /tmp/php-fpm php_admin_value[upload_tmp_dir] = /tmp/php-fpm env[TMP] = /tmp/php-fpm env[TMPDIR] = /tmp/php-fpm env[TEMP] = /tmp/php-fpm