We don't currently test with SQL server during development - we primarily test with MySQL and Oracle, however, there are several others who have been succesful with other db's. Maybe they can comment on whether they've seen the same issues. Could you raise a JIRA bug?
For your follow-up question:
You can configure the data that is imported into the Repository during the bootstrap phase by changing the following file (in PR5):
/projects/repository/config/alfresco/application-context.xml
In here, you'll find a bean called 'importerBootstrap' which accepts a property called 'bootstrapViews'. Each view is a location to an XML file that contains the data to import. You can either remove, add or change these files.
The data files are also located in /projects/repository/config/alfresco.
Of course, if you do make changes, it is possible to break the Alfresco Web Client as it will be relying on some of that data, but for your own custom applications this is fine.