FlightGear 2016.1.1, Ubuntu 15.10
I noticed that ffgo lists parking positions for most airports, but for airports located in the default scenery area (KSFO, KSJC, KOAK, etc.) I could select parking but would always start on the runway regardless. I could start in parking just fine everywhere else (I fly out of CYYZ a lot, for example). Since I end up buzzing pilots that start up on KSFO 28R all the time, I thought this might help other users who are having this problem.
The fix was pretty simple, and obvious: delete the default scenery folder (or rename it, probably safer), then let TerraSync download the data for that area. And then voila! Can start on parking anywhere. I imagine the location of the folder varies by system, on mine it was in /usr/share/fgfs/Scenery (I think, going by memory).
Cheers!