Well, the System program feature is assigned to a specific port on the system. This can be changed so if when you press menu you no longer get the proper prompts, someone has changed this.
If you moved the phone via system renumber, the system prog port doesn't move with it. So if you did this, the sys prog port resides back where the extension used to be plugged in.
Otherwise, I know the first port on every card can be programmed as the system prog port. I think it is also the 5th port as well (but it could be the 4th, it's been awhile). Ports go from bottom to top on a Merlin Legend.