Since upgrading to FGFS 3.4 I also have (had) that problem, intermittently.
My system: ubuntu 15.04, 8 GB, OS 32 bit
I usually start with a command file (not changed since before 3.4!) - any plane starts nice on EDDF -->
but on runway - although --parkinglot is specified!)!! With FGrun I have/had the same problem - sometimes I could select the parking-lot - but it still placed me onto runway! Also I noticed that TerraSync did not start when trying to start on "new" airports (I could select that "new" airport in FGrun with selection "All airports" - but again I just get onto the runway -- AND after waiting 1/2h and restart that "new" airport is not shown in the FGrun list "installed airports". (BTW: I am sure I have only new scenery and "--enable-terrasync" is always active!)
I then
deleted the (hidden file) ".fgfs" in home directory - and it works with command-file! (originally that was taken over from former 3.2 FGFS!).
BUT: trying to then start with FGrun again does not work.
To get FGrun to place me on parkinglot - I again had to "Restore default settings" in FGrun
and that means the start with command-file does not work any more - I had to delete the ".fgfs" again to make that work
etc etc loop loop
There seems to be some (eng-) confusion about what the default scenery settings are (nowadays!).
At least I am able to "fly" again!
My summary: For the time being do not try to use sometimes FGrun and sometimes a command-file!