Tony,
Rollerball is correct about the hold short point. In addition to that, I would recommend placing a regular (blue) node right behind the hold short node (slightly farther from the runway.) I've noticed sometimes when a line forms at the departure runway, the aircraft at the front of the line will get stuck because it doesn't have a node to proceed to. Adding the blue node will fix this.
Regarding your aircraft disappearing, here are a few things to consider:
1. Is the aircraft used in the flight plan designed for AI traffic use? Not all aircraft are! I recommend not using aircraft designed in FSDS. Better to stick with GMAX-designed aircraft.
2. If an aircraft is not showing up at its scheduled arrival time, make sure you are setting your clock according to Greenwich Mean Time. All AI flight plans use GMT.
3. If planes are disappearing after getting taxi clearance, that usually means that their parking space is not connected to the taxiway system in AFCAD.
4. If you're not sure which aircraft is assigned to a particular flight plan, best thing is to look up the plan in your traffic editing program and see what it says. With some programs, it may be necessary to open the Aircraft.txt file and manually add a new aircraft entry before compiling for the flight plan to be assigned to the new aircraft.
Hope this has helped!
Good luck!

Erik