I just got bit by this recenty. ALWAYS run prescan.exe on your SharePoint 2003 environment before you migrate to MOSS 2007. Prescan prepares the database for upgrade. In particular, it parses and saves list definitions with the associated lists, as well as reports any errors that will cause the upgrade to fail. I have already done 2 SharePoint 2003 to MOSS 2007 migrations in a test environment and things moved over pretty well (I did this to document the post migration steps required for our environment - VERY GOOD PRACTICE). Finally when we were migrating to stage -- upon attaching the database using stsadm I got the following error.
"The [Databasename] on [servername] contains user defined schema. Databases must be empty before they must be used. Delete all tables, stored procedures and other objects or use a different database".
After going over what we did differently this time, we realized that we had forgotten to run prescan that day before backing up and moving the database. So we did exactly that and the migration to stage went as expected.
So run prescan early and often if you are migrating to MOSS 2007.