I tried the option to write out the native_fdm to a file from the Windows 1.0 release of flightgear, and loaded the result into matlab.   Initially I thought there was a structure with a regular size of 408 bytes, and I was able to extract altitude correctly from the first few dozen instances, but that seemed to change as the simulation progressed and it all got out of sync.  Is there a byte or two being sent in addition to the FGNetFDM structure that is not sent every update?