The thing is, you already connected and used mysql connection, so changing the config doesn't do anything, unless you purge that connection. A short example:
// Use mysql
[1] > DB::setDefaultConnection('mysql');
// NULL
// Check the prefix
[2] > DB::getTablePrefix();
// ''
[3] > $first = DB::connection('mysql');
// object(Illuminate\Database\MySqlConnection)(
//
// )
// Change the prefix
[4] > Config::set('database.connections.mysql.prefix', 'some_prefix');
// NULL
[5] > $second = DB::connection('mysql');
// object(Illuminate\Database\MySqlConnection)(
//
// )
// Check the prefix again - no change..
[6] > DB::getTablePrefix();
// ''
// Because the connection is just the same object
[7] > $first===$second;
// true
// So let's disconnect and destroy it
[8] > DB::purge('mysql');
// NULL
[9] > $third = DB::connection('mysql');
// object(Illuminate\Database\MySqlConnection)(
//
// )
// Now check the prefix - it's good
[10] > DB::getTablePrefix();
// 'some_prefix'
// And the connections are different
[11] > $first===$third;
// false
Btw, you can wait a little bit for my multi-tenancy package that I'm working on ;)