I think Usda's issue is coming from along experience with games where armor makes you harder to hit, as opposed to SR where armor makes you harder to damage.
A hit in Shadowrun just means you've connected with your target. Nothing more, nothing less. If you hit well (have lots of net hits left over) you greatly increase your chances of making it a damaging strike -- but because there are dice involved, it's no guarantee. Sometimes in real life, a guy takes a solid punch and just keeps coming. Should Mike Tyson or Brock Lesnar always be taking a box of damage, when a little old lady hits them with her purse?
If your gaming group wants to house rule it so anytime you're hit with lethal damage, you take at least one box? Knock yourself out. I could see it adding some realism to the game, so that even the hardiest Troll in the heaviest armor can still get "nickled and dimed" a little bit. I think the game's lethal enough as it is, for the most part, so I wouldn't want that sort of house rule in my game...but as I recall, your group's got at least one fairly min/maxed soak machine, so maybe you're having a different experience with it than some groups.