Using l2gen from the SeaDAS command line gives the following error, which does not seem to affect anything:

SeaDAS> l2gen, ifile=l1b_file, geofile=geo_file, ofile1=l2_file, l2prod1=['chlor_a'] $
SeaDAS>         ,/metsearch, /ozonesearch, /sstsearch, /icesearch, proc_ocean=2, /WAIT
GENERIC_FILE_TYPE detected a MODIS file.
sh: /opt/seadas6.4/run/bin3/ncdump: No such file or directory
Detected a high-resolution file.
and then it continues on.

I don't get the error when I use the GUI.  It is easily fixed by issuing the following command:
ln -s linux_64/ncdump_hdf ncdump
in directory $SEADAS/run/bin3

This might also have been an issue in SeaDAS6.3, since I have the same symlink there.

This is on a CentOS5.8 system.

There are two files where I missed converting ncdump to ncdump_hdf:
l2gen_main.pro
l2gen_pfile.pro
search for ncdump and change the lines appropriately.

(the GUI works because l2gen_screen.pro was corrected...)

Sean