I am comparing databases and scripts using only SQL Server 2000. The scripts were made from SQL 2000 databases. Somewhere along the way I started getting the error that one side had schemas (corresponding to users) that the other did not. I have had to edit all my projects to uncheck Schema comparisons.
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Did, at some point, one of your scripts get compared with its version set to 2005? You can set a 2000-sourced script's version to 2005, and this will produce schemas from the users in the manner you describe.
If you have synchronized to a script while it is set to 2005 mode, then SQL Compare may have generated actual CREATE SCHEMA statements, which you will have to remove by hand. Otherwise, you can fix the problem by ensuring that the script is set to 2000 mode (you can set this in the projects individually, and if new projects with the script keep returning to 2005, you can manually set the default version for the script folder by editing the SqlCompareDatabaseInfo.xml file - DatabaseVersion is 9 for 2005 and 8 for 2000).
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