Mathis,
We've created a new version of the netCDF package that fixes the 1999
nc_sync() bug but shouldn't have the performance problem that you
encountered.
Would you be willing to test it? The new version is available via
anonymous FTP at
ftp://ftp.unidata.ucar.edu/pub/netcdf/exp/netcdf-3.5.1-beta12.tar.Z
Please let us know what you decide or discover.
Regards,
Steve Emmerson