On an upgraded system now running the latest (MT4.01) everything seems to work right except the publish site option. On any of the blogs in the installation running a full publish gives the following error when publishing Index Only.
Non-numerics in limit/offset clause (20 , 0) at lib/MT/ObjectDriver/SQL.pm line 262.
I added the EntriesPerRebuild to the mt-config.cgi just in case but it has no effect. I'm off to start deleting index templates to see if one in particular causes problems...
