I'm new to the Phenom 3000, but I've had no problem with the G1000 on other planes.  When I enter a flight plan I always enter my departure airport first.  I then continue adding way points.  Randomly, after entering a way point, it will remove the departure airport from the list, showing only the way point I added so far.  I tried this with 2 different flight plans and had the same problem both times.  What am I doing wrong?

What Nav extension do you have installed?  1.2 was giving me issues with putting the same altitude for every sid/waypoint/star, just flat across the board. So i rolled back to 1.1, but I think its causing my P3d v3 to crash, but not certain on that.   What Sim are you using? what versions of the plane/nav extension are installed?  I would submit them a ticket, they are pretty good with getting back to you.