Say I have a pain compensator bioware, rating 6. Does that mean I ignore 6 boxes of Physical and 6 boxes of Stun, or 6 boxes of Physical or Stun, before applying penalties? I would guess the latter, but I'm not quite sure.

Also, didn't Fanpro used to have a costumer service line for Shadowrun? Why can't I find it?

Thanks!

As I understand it, the boxes are still the boxes, but the negative modifiers don't start racking up until the compensation level is reached.

So, a runner with eleven boxes and a Rating 4 pain compensator would take a penalty of -1 at seven boxes, -2 at ten boxes, and fall unconscious at eleven.

He's still wounded. He can just ignore the effects of those wounds ... up to a limit. Damage Compensators do not grant more actual damage-taking capability (as reflected in the damage track itself), so the dude with the implants would keel over when he reaches his Damage Track maximum, just like normal.

I think the clause that's being missed here is "before determining injury modifiers." Unconsciousness is not, to my knowledge, an injury modifier.

The rules go out of their way to stress both, as opposed to either/or.

That depends... the implant does not use a capitalized game term.
M&M had rules concerning that point, Augmention missed them.

If you rule it that way, getting a Pain Editor of Trauma dampener will give you better results for less Essence.