The problem was caused by "itemperature" and "idensity" turned off in the AEM3D configuration file.
I have turned out these features hoping, that it will speed up tests with various bathymetry inputs. It worked well until I have used a bathymetry input file with variable dX and dY.
Such bathymetry file can be used, but the "itemperature" or "idensity" has to be turned on first.
The problem is solved.
Nonetheless, I have snet my input files, in case you would like to have a closer look.
Rafal