If your hypothesis is correct, which it most likely is, that the switch controls one of the outlets, then the extra pair of wires in that outlet have to do with the switch. Either they provide a separate loop to control just one half of the outlet (some switched outlets are like that: a switch just controls one of the receptacles out of the pair). Or else the extra wires are meant to be in series with the outlet, going out to the switch.
It sounds as if you miswired it so that the switch hookup is in parallel with a receptacle's hot and neutral (thinking that it's a daisy chain connection to the next outlet).
When you do that, guess what happens. Everything works when the switch is open, and when you close it, it short circuits.
A half-switched outlet, if that's what your friend has, normally requires three connections (not including ground). Two wires will come from the breaker, and two from the switch giving you four. This means two of them get connected together. How this happens is that the switch receives hot, and so it screwed to the same terminal as hot, or otherwise spliced to hot. The return wire from the switch feeds the secondary hot that controls the switched part of the receptacle.
The best way to proceed here is to turn the power off at the breaker and verify continuities: in particular, which pair of wires corresponds to the switch. With the power on, you should also check that you haven't wired any outlet with the opposite polarity: neutral being hot and vice versa.
It would have been simpler to just connect the bottom outlet's live (the black) to the top outlet live on each pair.
The switched live wire (red normally) should be connected through to the end and labeled in each spot (this allows the next guy to restore some outlets to the switched setup).
Best Answer
Double check the first 4 outlets that you rewired. You probably have the wires swapped or touching. Something like the black and white wires swapped, or a bare ground wire touching the side of the screw terminals on the side of the outlet.