There are 2 pots I believe that are set to deliver all the tones in the system.You can "play" with them but it will affect all the tones (busy,ringing reorder,dial tone).Don't know that I would suggest it but it can be done somewhat.It is not meant to be though.Hmm Co 1 and 2 are built into the motherbaord but at least you do have the extra cards installed.
As for the keys programming are you sure you don't have duplicate keys on the sets in question?