That is weird, PA should protect you from minigun fire- they only do 7-11 damage a bullet, and PA's damage threshold is 12. You really shouldn't be taking any damage... IIRC, JHP ammo's damage modifier is applied after the initial damage calculation, so that can't be the problem.
Like Silencer said, maybe it's a bug... the levels of damage you're taking sound more like you're wearing combat armor, if anything. Any chance we can get a screenshot of your DT/resistances, or maybe you can just post what they are?
You just got the Alien Blaster, huh? It's a good weapon. If you're still using a Sniper Rifle like you said earlier, I'd recommend switching in the AB. If you have the Energy Weapons skill, that is.
Edit: Don't think there are any spoilers this time, heh.