When configuring a Farm or creating Web application using pre-configured databases, psconfig, stsadm -o extendvs, stsadm -o createssp and other related commands run successfully but you will see bunch of 3759 errors in the Event log.

Event Type:            Error
Event Source:         Windows SharePoint Services 3
Event Category:      Database
Event ID:                3759
Date:                       12/12/2007
Time:                       2:46:01 PM
User:                       N/A
Computer:               HQS560
Description:

Database 'MySite_Content' on SQL Server instance 'SqlShareDev' is not empty and does not match current database schema. 

After looking into ULS logs it turned out that 3759 is a result of sqlexception(s) happening during the provisioning since the Setup user and the Farm Admin accounts in this type of deployment usually do not have "securityadmin" and "dbcreator" sql rights.

In my case I managed to configure the farm successfully and simply omit the error :)