It's ALIVE! It works perfectly and it was exactly the first issue that A55A55IN pointed out - adaptations. I think it's a battle of ignorance. I was ignorant of exactly which adaptations to clear, the European auto shop that I had clear them with the Motec and Autologic systems either didn't know, or the machines were incapable of clearing these adaptations. Then, the BMW dealership must not have known which adaptations to clear.
Basically, I spent $200 at various shops and the dealership trying to get these things cleared. Active sent me one of their actual laptops - which turns out to be a standard PC with a USB-CAN adapter running an older version of the BMW software on it. Plugged it in, hit "Reset Adaptations" and we were in business.
Hard to believe they can make this kind of difference. At idle, running the Stage 1.5 tune I was seeing (+)30-40% fuel trims. After the reset, (-)25-30%. Seeing this, I flashed it back to the stock Stage 2 tune and am now seeing (-)4-10% even under load. No rough idle, and it comes back to idle no problems (doesn't die).
Thanks to Zak over at Active for letting me keep him on the phone for an hour on Friday evening. Also - I've never had Zak not respond to an email or a phone call. He's on top of it. Going to arrange some dyno time this week and get it final tuned. I'll keep you guys updated.