I have seen a few threads like this and if you search about the ATP TS2 you will find a few more posts of people having similar issues. Unfortunately you will find that they tell you to send it back and get the reflash, and I know of two who have done this and were told they had the most recent flash. So....what is the real issue? I've not been involved intimately with the install of either of these ignitions, but find it odd that people keep having the same issue and the company doesn't seem to think there is an issue. At least not from what I've seen/heard. I've personally seen/installed the bendix and flywheel on one ski and if it is not a programming issue then logic would lead me to believe it's a machining issue with the ring gear. Regardless, there appears to be a real issue.
Before anyone asks, the tune is very mild and has low initial timing at startup.
In my friend's case it cost him real money to send the ignition across the pond, and then they had to pay to have it sent back, only to be told that it was fine. Oh, and they sat on it for weeks before returning....in fact I'm not even sure it's been returned.
I'm sorry I can't help you with the issue more, but I hope others will chime in if they are having similar issues. Based on my admittedly limited secondhand experience with ATP's customer service, I'm not impressed.