Beta 3 Standard Edition + Derby

According to the text on the Downloads page, only the Express-C version still supports Derby. You'll need to trade up to DB2 to use Standard edition.

It will be possible for a team of up to 10 users to use Derby with the Express and Standard versions of Team Concert. If your team size is greater than 10 you will need to upgrade to either DB2 or Oracle.

We are working to make these changes happen now, and once the builds have been updated we will be updating the download page as well.

After my research, I found the way to resolve your problem:
The default configuration is to use DB2 database. In order to use Derby, you should do like this steps(in Windows platform):
1. Modify the teamserver.properties under <installDir>\jazz\server folder,
uncomment the following lines for Derby configuration as below:
#
# DERBY Configuration
#

# JDBC DB location, specifying this property disables system-based selection of default location
com.ibm.team.repository.db.vendor = DERBY
com.ibm.team.repository.db.jdbc.location = repositoryDB

Comment the lines for DB2 configuration as below:
#
# DB2 configuration
#

# Comment out above lines, uncomment the following three lines and customize example location to use DB2
#com.ibm.team.repository.db.vendor = DB2
#com.ibm.team.repository.db.jdbc.location=//localhost:50000/JAZZ:fullyMaterializeLobData=false;user=jazzDBuser;password={password};
#com.ibm.team.repository.db.jdbc.password=jazzDBpswd

2. Launch CMD window.
3. enter <installDir>\jazz\server folder, execute "repotools.bat -createTables" command.
4. Open the setup wizard to configure your server using the url https://localhost:9443/jazz/setup.
5. Choose Custom Setup, select Database Verdor as Derby, Connection Type as JDBC and JDBC location as repositoryDB, then click test connection button, it should work for you now.
NOTE: Maybe choosing Fast Path Setup is more convenient, but I didn't try.

All the other DB2 confirgurations should also be added "#" comment mark besides the DB2 configuration I metioned in my last reply. But I seems no matter to create the table if you didn't comment the other.