I think there were some issues with SH3 Commander and NYGM. Check the SH3 Commander FAQ or send an e-mail/PM to Jaesen Jones. I'm sure it was discussed before but I couldn't find the link. I'll have a look though again
http://www.users.on.net/~jscones/software/products.html
EDIT: Check out this thread. I think the NYGM issue is discussed there
http://www.subsim.com/radioroom/showthread.php?t=95448