In VATS, each shot will do a set amount of damage, regardless of what body part you target, or if you crit.
AFAIK, there isn't a fix out there, so I have been searching for one.
The problem seems to happen because the gauss projectile has an explosion on it. Remove the explosion, and it works fine. But I, and many, many people out there love that explosion.
More on my progress later...