This usually indicates that a previous start of the server was able to create the database and the core schema, but failed (or was stopped prematurely) in the process of creating all the tables. Now that you've resolved the other issues preventing startup, I suggest you:

• Shut down Tomcat
• Delete your labkey database
• Start Tomcat

LabKey should automatically create the database, schemas, and tables, and then populate tables with data.

Adam