I have managed to solve the problem:
At first, I was importing river geometries from SHP files generated in ArcGIS; well, I think this operation was producing some topological errors, for example in junctions. By editing the river layer directly in RasMapper with identical paths to those present in the SHP files, the problem has been solved. I can now properly save the g01.hdf file with all the geometries (banks, flowpaths, etc.) and continue the work without this problem.