I thought that the ground elevation should change regardless of the flying altitude (dependent only on lat lon data)
yep that's the case here, i didn't notice it was a ground elevation altitude
it can be stuck at the same altitude if you're immobile, on a very flat land or if it take the altitude on a 3d model flying at the same altitude.
here the ground altitude change in FG for a ksfo landing in external fdm, with the latest FG version compatible with simulink net_fdm (2020.3) so i can't be of much help for your case, given both the net_fdm and net_ctrl procols seems to be working.
any reason you're still using FG 3.4 ?