I have come across this issue whilst trying to sort out missing user roles in the various places within the admin that you can change the roles (the drop down list contains only wiki-editor as a role, no subscriber, editor etc), which we had put down to an incompatibility with Wiki Editor plugin.
In an attempt to see whether the DB was fragged or the file structure, I installed a virginal copy of 3.01, then swapped our DB for the one thats created by default.
Reloading causes a DB connection problem, going into wp-admin produces the prompt to repair the db, doing so shows that wp-posts through to wp-taxonomy etc are missing.
Anyone with any knowledge of WPMU pre to its amalgamation in WP 3.0 series be able to tell me if I'm correct here; but - given our original installation was pure WPMU - the default blog/site is wp_1 isn't it? Not wp_?
To test the theory, I copied over all the wp_blah tables into the DB for our install ( a copy) and WP kicked in no fuss, well, a bit of whinging about certain tables not being closed by users.
However of course, there isn't a wp_ in our site installation, so the default blog is blank.
All the user roles are back in again! Just not sure this is a neat way of fixing this.
Andrea and Co - any ideas?
best wishes and thanks in advance
Steve / Nibb