So you own your own StarScan Tool?
Its sounds like you need the advice of someone that is an expert in the StarScan tool and likely your the only one on this forum that owns a StarScan Tool, so you're NOT likely to find it.
Has a bunch of Forums for Chrysler/Dodge/Jeep vehicles, there are several experienced Chrysler techs that know about the StarScan tools that often post there, might be your best bet, go there and post your problem.
Is it possible it doesn't have all the updates for the tool, and thus it did something it shouldn't have for a later model vehicle than the update?
BTW, what year vehicle did you do this procedure on, and what was the latest updates to your StarScan?
When I got new FOBIK keys programmed to my vehicle, the dealer told me I had to bring all the keys (programmed and unprogrammed) with me to program the new keys. I have a 2010. I got the impression that they do something to the effect of reseting the WIN or SKIM to eliminate lost keys, re-enter existing keys and enter new keys. BUT, I'm only guessing.
BTW, how did you come by a StarScan tool, did you pay the thousands of dollar for one? OR did you luck into some deal, I'd love to get one myself, but could never afford the price.