Ok guys, I need help!

I first used the V2 to program my 05 LLY duramax 3 months ago. Since then the batteries have been disconnected several times. Now I want to install a stock tune with stock tires for winter, but I am having all sorts of issues.

When I plugged the V2 in, it first said something about licensing the controller, but I did that months ago, so I said yes. Then i got all sorts of connection issues, 028something so I did a firmware update, Now I am at 2.06.41, was at 2.06.40.

Then I tried uninstalling all efi stuff from the computer and reinstalled V8 and 7.5 software, did an update search and install. I also formatted the internal and sd memory in the V2.

Now when I try to install the tune, I get $0322. When I try to read the tune, I get $0312.

As I said the firmware is 2.06.41 and the bootblock is 2.06.03.

I probably didn't do something right, so that is why I am here!

Also, when a new firmware is installed, do all previous saved tunes need to be configured or something for the firmware update?