Ok, I think I figured out what was going on, and I was totally incorrect in my original assumption. The reason my anchor points looked incorrect is because the [convertPoint toNode] call was returning me Scene coordinates that were incorrect. After several hours I realized it was off by exactly half the screen dimensions. My Scene has an anchorPoint of (0.5, 0.5), but this screws up the conversion values. So, if I simply offset the point by width/2, height/2 it's correct:
GPoint pt = CGPointMake(anchorWorldX, anchorWorldY);
pt = [gGameScene convertPoint:pt fromNode:gGameWorld]; // convert to scene coords, but it's WRONG
pt.x += scene.size.width * scene.anchorPoint.x; // this properly adjusts the value to be correct
pt.y += scene.size.height * scene.anchorPoint.y;
SKPhysicsJointPin* pin =[SKPhysicsJointPin jointWithBodyA:hinge.physicsBody bodyB:door.physicsBody anchor:pt];