For some reason, the Nephilim's thrusters and all its weapon points are all off by a bit to its left. I've narrowed the problem down to the MediaVPs themselves. Irrespective of mod, if it uses the 2014 MediaVP Nephilim, it's offset. If it uses the retail one, (such as using an older media vps, or retail) it's normal, if ugly. Of course, when I inspect the .pof itself, everything is positioned properly. None of the other shivan strike craft are affected, nor anything else that I can tell. I re-downloaded MV_Assets to no avail.
I barely noticed it, but now that I have, it bothers me to no end. The subtle, unobtrusive nature of the bug as well as the fact that only one ship seems to be affected only baffle me further.