My theory (THEORY) is an O2 sensor. It's not working right until it actually is warmed enough. That is causing the emissions to go out of the acceptable range UNTIL it heats up enough... O2 sensors don't work until hot, did ya know that? Some even have their own internal heater...
Could also be the Cat, as that is heat sensitive too. Cat's don't work until they reach some astronomical temp like 500 or something...
randy