The Ids is pretty good about disconnect supervision there is an option on the M screen for how the system handles call when the drop pulse timer is met.You should set it to drop a line under the Talk condition.
As for the lights yes that is a problem with 3 digit extensions I believe it's the D screen on the VXC programming fpr mailboxes status.Set the message waiting lamp field to the 4 digit extension equivalent ie 312 =3012.