I have the same problem. WP Multisite (localhost and production), version 3.8. Version plugin: 3.1.1. PHP: 5.4.
Looking PHP errors on server, it appears when install this plugin:
PHP Warning: opendir(/home/domain/www/subfolder/wp-content/uploads/backwpup-4e6ec4-temp/): failed to open dir: No such file or directory in /home/domain/www/subfolder/wp-content/plugins/backwpup/inc/class-job.php on line 1977
This folder (backwpup-4e6ec4-temp) exists on server, with 755 permissions. I changed to 777, but occurs same bug (don't save jobs, settings, etc.).