SPManager ERROR [8/2/2012 10:00:27 AM]: An explicit DROP INDEX is not allowed on index 'Sites.Sites_Id'. It is being used for FOREIGN KEY constraint enforcement.
exec sp_helpconstraint 'sites'
Deletion the Foreign Key FK_lms_Categories_Sites
After that the Configuration completed successfully.
This is a known issue coming from the very old 2.x versions (when they were initially installed). SP alters index on ‘Sites’ table referenced by ‘lms_Category’ table when upgrading. To perform a successful upgrade it’s necessary to just delete the relation between these tables and run configuration wizard again.
This relation is not mandatory - it's necessary so that categories are deleted when organizations are deleted.
However, if you want to rebuild it you need to run the following script: