Various reports are coming from users with the plugin W3 Total Cache installed.
That plugin is very broken - the present count for users of the up-to-date WordPress version (3.5.1) on its plugin page - http://wordpress.org/extend/plugins/w3-total-cache/ - is 52 votes for working, 146 for broken.
You should turn off object cacheing, which is the broken part particularly affecting UpdraftPlus (and all other plugins which use WordPress's scheduler - hence all backup plugins that allow scheduling). You can leave page cacheing (which is the main speed gain for your site) on.
If you are using W3 Total Cache and have a bug report, then please first temporarily disable and/or remove it before posting bug reports against UpdraftPlus to confirm whether W3 Total Cache is the real cause of the problem - we've had several reports lately that we traced down to WP Total Cache's broken-ness.