The nofollow function stopped working after WP3.6 / WP3.6.1
I haven't yet tried the modified page.php file from this thread http://wordpress.org/support/topic/plugin-better-tag-cloud-the-plugin-is-full-of-errors
Instead used my own "GL Tag Cloud Nofollow" plugin to achieve the same result
Just thought I'd mention this if you're working on an update
Great plugin by the way...