07 Grand Prix PK3 Issues

I have owned my tuner for about a year and have kept a tune on the car for about that long. The only security box that I see with my editing software is how vats communicates which I set to none. Over time I had odd things happen when starting such as a slight stutter, the dic acting like it is seeing the car for the first time, the charging system failure warning on the dic even though the volt meter shows 14V, etc...

Car failed to start and after some troubleshooting the ignition switch was causing a short when going to crank (since some contacts open and some close at that time and that was not happening due to dead springs in the switch). I replaced the switch and would get the security message on the DIC and a no start. I just did a full write to put the VATS to have no communication, and now the car starts but will continue to show that message, while giving no way to get out of it.

Is there anything more that the tuner can do regarding this or do I have to go to someone who has a way to scan and configure a DIC?