I tried upgrading again with a local version. Upgrading from MU 2.7 to 2.8.1, I got several of these errors in the php error log:
[16-Jul-2009 09:58:37] WordPress database error Duplicate key name ‘taxonomy’ for query ALTER TABLE wp_21_term_taxonomy ADD KEY taxonomy (taxonomy) made by wp_upgrade, make_db_current_silent, dbDelta
The upgrade said it completed successfully, but I am still seeing the “WordPress MU 2.8.1 is available! Please update.” message.
Any thoughts?