I am successfully using SQL Server 2012 with CLM 6.0.5.  Is this the first time you are using SQL Server with CLM?  Were you running CLM previously with a different database?

With the information you provided it is difficult to know where your problem may be occurring. Did it occur on the Create Tables step for the first application (JTS) or earlier.

Some things to consider:
1. Environment Variable - have you configured environment variable SQLSERVER_JDBC_DRIVER_FILE?
In my setup the value for this variable is configured as: C:\Program Files\Microsoft JDBC Driver 4.1 for SQL Server\sqljdbc_4.1\enu\jre7\sqljdbc41.jar

2. Did you complete all of the database setup activities per" https://www.ibm.com/support/knowledgecenter/SSYMRC_6.0.5/com.ibm.jazz.install.doc/topics/t_s_server_installation_setup_sql.html ?

3. What path are you using for the database(s) in the Custom Setup steps:  For example - the following is mine for JTS

Database Vendor: SQL Server
Connection Type: JDBC
JDBC Password: ****
JDBC Location: //localhost\sqlexpress;database=jts;user=jtsDBuser;password={password}