The fileout netCDF-4 doesn't generate the correct dimensions for aggregated files

The fileout netCDF-4 output for a NcML aggregation of two NASA HDF5 files displays the wrong dimension information.

The correct ncdump output:

The fileout netcdf-4 output:

The original HDF5 files, NcML files etc can be found in the attached tar.

Hints:
1) The fileout netCDF-3 output for the same NcML aggregation gives the correct output.
2) The fileout netCDF-4 output of an HDF5 file gives the correct output.
3) Possibly there is a bug inside the netCDF-4 but definitely need to check.