A couple of things I've noticed: When I first installed the MT7 map in my bike after doing the exhaust system, I had a high idle speed for about 20-30 seconds, then it settled. When I took the bike in for replacement of the NIM module, I loaded the stock map back into the ECM before taking it to the dealer "just in case". My dealer is only about 5 miles from my house, so no big deal. When I got it back home, I loaded the MT7 map again, and it intially did the high idle speed again. After several starts and runs, it seems to me that the ECM is "learning" the new settings. Now when it's bone cold, it starts at about 14-16 hundred RPM, then quickly settles to 11-12 hundred. I always let my bike warm up for a couple of minutes while I put my helmet and gloves on before taking off, and don't turn the rpm's up until it's fully warmed up.
The bike has a "lope" to it when idling, but no miss. The RPM needle never sits totally still when my bike is idling, nor did it on my '06 with a 103".