I have been using this plugin for almost a year. When it works it is great! When I upgraded to WordPress 2.5 I started having a problem with the final two steps, reactivating the plugins and going to the final page. Before I could activate the plugins I had to upgrade the data base. Then I had to log back in to the blog. At this point the automatic plugin was lost and gave me a screen with "Are you sure you want to do this?" All the plugin could do at this point was to clean up the installation. I had to manually activate my plugins.
Today I figured out that if I remove the wp_nonce stuff at the end of the line I could get the automatic upgrade plugin to continue. Wp_nonce is a security feature. I think it is primarily used with forms but it can be used with links. About the only source on this function is the Writing Secure WordPress Plugins post by David Kierznowski. I think when I have to log back into WordPress, wp_nonce thinks I am breaking in and slams the door shut. From a plugin design standpoint I am not sure there is a need for this type of security at this point since all I want to do is activate my plugins and get my log report. I guess I will comment out lines 392-394 so the plugin will work.