I've just tried it now, can't reproduce it. Tied all the following:
- Going to LSGG, then opening the Flight planner to plan a flight from LSGG to LSZH, to purposely include 2 FSDT airports. Works.
- From the "Create Flight" screen, I've entered in the Flight Planner, creating the same plan as above. Works.
- Tried also loading a previously created plan, no problems either, and it moved correctly to the origin airport ( LSGG )
I'm using the latest FSDT software, the one that comes with PHNL, under Vista x64. Have you tried updating the Stand-Alone Addon Manager for FSX ?