Flashing the computer????

I asked a mechanic friend why my 1999 Explorer ran rough on start-up, and other times when cold. He said this was a computer issue and the dealer (for $75) or a local parts store (for $60) would "flash the computer" and this would clear up the problem. No CEL or codes showing, but it runs really rough on start-up, first thing in the morning. I replaced the plug wires, but this didn't help. 1999 Explorer XLS, pushrod V-6, 4WD, AT.

Anyone esle heard of this?