As Gargamel has noted, to use Commander and GWX together you need the config files for Commander+GWX. It comes as a small self-installer so once you have GWX and Commander both set up, the rest is almost painless.
SH3 Commander is here:
http://www.subsim.com/radioroom/down...o=file&id=2923
and the config files are here:
http://www.subsim.com/radioroom/down...o=file&id=1421