I can think of 2 possibles.

The LS1edit hardware interface is split into 2 parts.

Half has hardware that is supplied by the laptop's RS232 and it's voltage and handles RS232 protocol

The other half has hardware that is tied to the voltage of the car's ADLC connector and handle the PCM's functions.

When you leave the interface plugged in there still is a connection to the PCM and has not flushed the memory yet.
I could have just been without the memory flush that the engine then was tuned differently but old fuel trim stored averages.

Else without unplugging the interface the PCM had not thought transfer was completed and needed the battery of car disconnected for a few seconds.

By reflashing and pulling interface properly then all memory got properly flushed.

Always best to assure no voltage spikes to take any ADLC interface on/off before connecting to laptop with key off.

Also if in question is to pull one side of battery for a few seconds to assure flushing contents in PCM temp memory.