What I had to do when I added programs with the SCT was set the chip back to factory then re-install the programs. Only had to do this once after I had put in the charge motion plates and new gears, the system for what ever reason kept putting the car in failsafe mode it wouldnt read the new programs. I dont know about the hand held ones since I dont have one. But if that is all I have to do I am not going to complain it could be worse.

 

When you folks are doing the flashing using the predator, are you doing anything to the A/R ratio or timing? My thoughts are that if you do a global change to the timing curve or accidentaly put the A/R too lean or rich at any given RPM or range of RPM that the computer is cancelling out (going back to default) or toning down the program you put in to keep the Emission sensors happy or keep the engine from pinging/knocking.

http://www.alternativeauto.com/prods...tang_tune.html

Here's a link to tuning a 2005 Mustang. I think it's a little bias since they are explaining their service as well. Of course there is no info on the retuning that can happen after the fact but if you have a dyno and can see everything the car is doing then the program should stick. It does however have a good explanation of throttle by wire and how really computerized everything is.