I just upgraded to 3.1 and followed all the steps to do so with a manual upgrade. I deactivated all my plugins before doing so and went to reactivate them, only to discover that the plugins weren't being detected despite still being in /wp-content. The solution presented here(http://wordpress.org/support/topic/plugins-page-is-stripped-of-installed-plugins?replies=5) doesn't apply to me as I'm not using multisite. I've also tried the roundabout way of renaming my plugins folder, creating an empty plugins folder, and reverting everything back to normal. Still didn't work.