I think the log output you are seeing is from this line:
Configuration configuration = Configuration.getSharedConfiguration()
I.e. the default DataSource is loaded before you install yours. While there are ways to hack 3.0 startup sequence, I would strongly recommend instead to switch to Cayenne 3.1B2. It is on the verge of becoming "RC" and "final", so don't get alarmed by its current Beta status.
One way custom DataSource can be built in 3.1 is by defining a few properties in Cayenne DI module as described here, and letting Cayenne worry about the right startup sequence. Trimming the irrelevant parts of the advice above, you startup code might look like this:
Module m1 = new Module() {
@Override
public void configure(Binder binder) {
binder.bindMap(Constants.PROPERTIES_MAP)
.put(Constants.JDBC_DRIVER_PROPERTY, "com.my.Driver")
.put(Constants.JDBC_URL_PROPERTY, "jdbc://db1_url")
.put(Constants.JDBC_USERNAME_PROPERTY, "db1login")
.put(Constants.JDBC_PASSWORD_PROPERTY, "db1password");
}
};
ServerRuntime r1 = new ServerRuntime("cayenne-project.xml", m1);