The hardware setup was taken directly from MPGuino, so I know it's pretty solid. I have one arduino putting a test pulse train out on pin 2 - 2ms on, 98ms off, for example (same as 2ms of fuel at 1200 RPMs, since the injector fires every other cycle). Pin 2 on the test signal generator is linked to a 22k resistor to pin 2+3 on the target, with a 5.6v zener to ground (for protection from injector flyback,etc). Ground pin on both boards are linked with a straight jumper, about 4 inches long.
In the car it seems to work fine, so I'm not concerned, but when I have the test generator powered by USB on my PC and the target board powered by USB on a laptop (not even plugged in), it gives weird results.
Again, it works fine in the car, it's just strange.