Hi Michael:i dont see any unused dimensions in the test file, but see them in the other file, so i assume they didnt get added. when in doubt, use the c library ncdump utility
it might be a bug in my code, can you use the latest version of the library (2.2.10) and try again? If that fails, send me your code that creates the file.
http://www.unidata.ucar.edu/content/software/netcdf-java/index.html FYI, we prefer ".nc" for binary netcdf files, "cdf" for a similar file format from NASA: http://cdf.gsfc.nasa.gov/