Michael,
In JIRA HB-819 
http://opensource.atlassian.com/projects/hibernate/browse/HB-819?page=all 
you say you fixed this once, do you still have the fix?
This is causing me problems with SQL Server, I can't use SchemaExport to create the tables. I have to generate a script then use SQl Query Analyzer to run the script, a real pain.
I also see that HB-819 was recently changed from a Bug[1] to Improvement [ 4 ].  IMHO, this issue should have a higher priority as it effectively prevents using SchemaExport with SQL Server.  With SQL Server you need to have your tables owned by 'dbo'.