It seems that updating the SCT software has corrupted the strategy tunes.
In that case I suggest you contact Brenspeed and ask them to provide you with a custom tune (for a small fee of course). This will solve your problem once and for all.
Before you upload the new tune, I recommend that you thoroughly clean the inside of the throttle body especially around the throttle blade 'cause even a small amount of dirt can cause idle issues.
No one is listening lol its not that hard....call SCT!!! They will look over the tune and tell you the problem. May take 30 mins on hold because they're always busy but you won't regret it just give them a call