I have experienced something similar, having loaded the 2 mods. never had any CTD problems before (except with the auto crew positions which I no longer use).
I thought the problem might be with SH3 Commander though and so I ahve taken to only loading the game using SH3 Commander at the beginning of each patrol and not using it to load mid-patrol saves as i used to.
I no longer get the CTD at the end f the loading screen now.
Still not sure if it is the mods or SH3 Commander, and although my OCD is going mad I can live with my work-around.
LJ