Originally Posted by Dunner
Just a WAG, but could it be that the ECU is telling one injector to stay open longer when it is cold? Although it will run rough, try pulling one injector connector at a time and sniffing the exhaust after it has a chance to clear out any excess gas. I have seen one ECU that was keeping one injector wide open and the engine was running pig butt rich. You could also do this with a scope and comparing the pulse pattern on each injector.
This is called "sequential" injection and it's unusual on gas motors and fairly new. It's sequencing the injector fire with valve position. Perhaps common in diesels, but it produces moderate benefits in gas motors.
It's much more common to have injectors fire in "banks" - that is, the entire side of the motor fires.
That doesn't mean that a single injector cannot get stuck (like it did on my 454 Mag MPI), but this was an injector fault, not an ECU fault.