When the engine is still cold, the ECU resorts to a preset air/fuel map . When the engine warms to its normal operating temperature, the ECU starts paying attention to the MAF and knock sensors and what-not in order to adjust the air/fuel ratio on the fly.

Your MAF sensor could be shot, giving the ECU false readings (or no readings, for that matter). If you are getting check engine codes for the knock sensors, then that is almost certainly your problem though. When the knock sensors notice detonation or start to go downhill, the engine will retard the timing in order to keep things safe for your engine internals.

This would explain why the car ran a little better after the ECU memory had been cleared... It hadn't yet decided on whether or not the knock sensors were bad.