Some program settings will affect your connection. Most commonly these programs are security software like BT PC Security. These are intended to protect you online and don't normally affect your connection in any way.
That said almost any program that uses the internet has settings that can affect your connection. This can vary from the BT PC Security firewall being set to update or Microsoft Windows being set to download automatically taking up some of your connection speed.
If you think a program may be affecting your broadband you'll find it's often difficult to pin down the culprit. A good rule of thumb is to try and disable the program and see if the broadband connection improves. If it does it's likely a setting in that program is affecting your connection.