Hello,
Please do a ref/sync capture. Please name it something relevant and not "ref sync capture", I have a million of those.
Let's go back to basics and work from there. You cannot just set the number of ref teeth to whatever gets the engine to do something, this is just leading down a path with no happy ending. The original LS1 mode is definitely 24 teeth and the later is 60-2 so 12 teeth is not going to help anything.
There are two different crank sensors for the LS engines that are not interchangeable, an LS1 (24tooth) and an LS3 (60-2). If you get them mixed up you will have all sorts of issues. I have even bought the right part number before but got the wrong sensor.
We have been running LS engines wasted spark on Hundred series and M84s for years so there is nothing fundamentally wrong with what the ECU does.