This post is an FYI to plugin developers. According to Scribu who posted on the WordPress development update blog, If you were using register_activation_hook() to also handle updates from older versions of your plugins, you will not be able to do so any more in WP 3.1: [16012]The activation hook is now fired only when the user activates the plugin and not when an automatic plugin update occurs. This is consistent with how the deactivation hook works.. There is a proposal for a register_update_hook instead within ticket 14912.
All plugin authors should read the post and the associated tickets to make sure your plugin will check for updates properly after WordPress 3.1 is released.
I provided a detailed follow-up that explains the rationale and decision-making process behind this, as there was some initial confusion.