I did read FAQ #11. ExifTool.exe, .ExifTool_config and the photos are all in the same directory. No changes were made to the .ExifTool_config, except to add: print "LOADED!\n";

"Loaded" does appear when I execute the batch file.

(Don't laugh) To add custom tags I was renaming the executable to:
exiftool(exiftool -v3 -NewIPTCTag=Phylogeny -k -P).exe
for each custom tag

I also tried a batch file that looks like this:

exiftool [IPTC:]Taxon+=Archaeognatha -overwrite_original -P
exiftool [IPTC:]TaxonCode+=value -overwrite_original -P
exiftool [IPTC:]Phylogeny+=value -overwrite_original -P
exiftool [IPTC:]Order+=value -overwrite_original -P
exiftool [IPTC:]Family+=value -overwrite_original -P
exiftool [IPTC:]Genus+=value -overwrite_original -P
exiftool [IPTC:]Species+=value -overwrite_original -P
exiftool [IPTC:]CommonName+=value -overwrite_original -P
exiftool [IPTC:]Description+=value -overwrite_original -P
exiftool [IPTC:]IdentificationBy+=value -overwrite_original -P
exiftool [IPTC:]Country+=value -overwrite_original -P
exiftool [IPTC:]State+=value -overwrite_original -P
exiftool [IPTC:]County+=value -overwrite_original -P
exiftool [IPTC:]CountyCode+=value -overwrite_original -P
exiftool [IPTC:]Locality+=value -overwrite_original -P
exiftool [IPTC:]LocalityCode+=value -overwrite_original -P
exiftool [IPTC:]Sublocation+=value -overwrite_original -P
exiftool [IPTC:]GPS+=value -overwrite_original -P
exiftool [IPTC:]Importance+=value -overwrite_original -P
exiftool [IPTC:]Control+=value -overwrite_original -P
exiftool [IPTC:]Range+=value -overwrite_original -P
exiftool [IPTC:]FlightPeriod+=value -overwrite_original -P
exiftool [IPTC:]Food+=value -overwrite_original -P
exiftool [IPTC:]Development+=value -overwrite_original -P
exiftool [IPTC:]PhotoQuality+=value -overwrite_original -P
exiftool [IPTC:]Aspect+=value -overwrite_original -P
exiftool [IPTC:]Disposition+=value -overwrite_original -P
exiftool [IPTC:]Photographer+=value -overwrite_original -P
exiftool [IPTC:]Keywords+=value -overwrite_original -P
exiftool [IPTC:]Comments+=value -overwrite_original -P

- Eddie Dunbar