A good test would be to use the console to remove your commando and sniper perks mid-fight, while you have a foe at mid-range like this, and see if VATS drops even lower if you try it again without the perks.
If its the same as before, theres a problem. If the new values are even lower, well, its probably not a bug at that point. VATS does lose reliability at a distance... Your situation seems to hint theres a problem, but its really worth testing to see if your perks are working.
Yeah, I just got back from grabbing some caffeine and that is what I was going to try. Hopefully they do lower and the problem is elsewhere
Edit: I guess I didn't remember properly, but the distances were a little more than the steps I listed above. This time I did a tcai and measured, about five steps is where accuracy starts dropping. I did one vats with all perks and all weapons at three ranges. one at seven steps, one at 20 steps, and one at 40. at seven steps I had 93% torso, 85% head, 95 on all limbs, without perks the numbers were almost identical(dropped a few percent all around but limbs were higher than head). At 20 steps head dropped to <50, limbs were over 85 and torso was at 77, without perks THE HEAD HIT % WENT UP. It actually, from the same exact spot I was standing at, went from %47 to %60 by just removing the perks. and at 40 steps more of the same, limbs and torso were over 50 with perks, head was below 20, dropped the perks and suddenly the limbs drop down but the head goes up.