Here's what I use:
<?xml version="1.0"?>
<nj22Config>
<ioServiceProvider class="ucar.nc2.iosp.gempak.GempakSurfaceIOSP"/>
</nj22Config>
for toolsUI (in my ~/.unidata directory). You'll need the fixes I
checked in this morning in iosp.mcidas or else you won't be able to
open GEMPAK files once you add the above.
Unless you are changing GridIndex, this shouldn't be a problem.
There are multiple projections in the file, but each is in it's
own group. I think the netCDF file specs are okay, but that the
CoordSysBuilder is picking up the projection type from the first
one in the file. It looks like they all end up as Lambert Conformal.
For a single projection in a file, it works fine. I don't have
any samples though. This has been a long standing problem (although
it used to be worse), so I don't think it's anything you've changed.