I can confirm I have the same problem with the latest Adrotate (or maybe the latest changes have not been pushed to WordPress plugin site?). I have a few millions entries in wp_options, which in my case is not a problem in itself, but it’s the high CPU usage that cause an issueby slowing down the website. Sometimes I can barely access the admin dashboard in wordpress.
The maintenance tab still shows the transients have been cleaned from time to time: “Clean Transients January 27, 2017 13:29”. It looks like it happens twice a day maybe.