I recently came across a problem where my main blog in a 3.1 multisite, buddypress setup was having issues displaying pages and posts. I must have installed every permalink fixer plugin in the repository trying to fix it over the last 2 days!!!
Then I went and renamed my plugin folder to just get rid of all the plugins...still no luck. I then started going through one plugin at a time and EVERYTIME I deactivated a Network Activated plugin I would RESET the permalink settings.
The Wiki plugin Network Activated was the culprit. When I deactivated this plugin and reset permalinks it worked. Simply deactivating the plugin without resetting permalinks resulted in still broken pages and posts.
Does the wiki plugin tie into permalinks in anyway??