MU Upgrade 3.0.5 > 3.1 Admin Stopped Working, Plugins Hard to Find

I ran a number of single site WP 3.1 upgrades from 3.0.5 without incident, but ran into very thorny problems with an WP MU upgrade. After the auto upgrade the admin would not recognize me as an admin user, left me in a very odd state at the “Network Administration” screen with only a dashboard on one other icon (can’t recall which), saying “Howdy,” without a name. Clearly had lost track of users. The site was still running fine on the user side, but any attempt to login to the site resulted in same strange behavior and the meta menu also seemed confused, still presenting “login” after I was logged in.

I decided it might be a plugin conflict and moved all plugins to an alternate directory. Sure enough, the site started working for admin, but of course all sorts of plugin dependent functionality was broken. But then the really odd thing: I moved all the plugins back and reactivated the same set that had been active before the upgrade. Everything worked. Both user and admin side are now fine.

However, there seems to be one “feature” of WP MU 3.1 that I really don’t like: all the “network active” plugins no longer appear AT ALL on the individual site plugin pages. The INACTIVE plugins do appear, but the ones I activated on the network side are invisible from the individual site side. This is terrible, since users can no longer tell which plugins have been installed and activated for them by just looking at the site plugins, they have no easy access to the “plugin site” links for documentation, etc. PLEASE bring the network active plugins back on the individual site pages!

Meanwhile, it seems my trouble upgrading was also somehow related to this plugin dance. I don’t know why removing and returning the plugins cleaned up WP MU’s confusion, but it seemed to do the trick. This would suggest something of that cleanup was missing from the auto-upgrade.