I was even more of an moron than I thought! I had SH3 Gen pulling from my default SH3 install instead of GW or NYGM!
I fixed the path and loaded it up for GW and it showed me task force starting positions all over the place. Than though, SH3 crashed on me for some reason. Not sure if it's related to SH3Gen or not, I'll try to replicate it today.