Hi all,
The default format for octave-netcdf is netcdf4 (as in matlab). I guess that you have multiple versions of ncdump on your system and one without netcdf4 support and one with netcdf4 support (as you where able to compile octave-netcdf).
Can you try with ncdump which includes netcdf4 support? To avoid future issues, i would suggest you to uninstall the old versions of netcdf (including corresponding utilities likes ncdump, ncgen, nc-config) without netcdf4 support.
Regards,
Alex