Normally with Idle problems I have learned that the farther your Tune is away from stock..the more time and effort you will spend trying to track the problem down. These Tables will build upon one another and you will end up spending days or weeks trying to figure it out...I know that is not always possible when your intake/TB are not stock.
That being said, I totally agree with TAZ that you have inadvertently disabled the Learning Parameters. The only other issue would be your Desired Airflow. Any way to smooth out those values? You can check out a little Idle Tutorial that will at least give you a pathway to follow. Check under GEN III stickies.
It definitely sounds like an Airflow problem, or worst case an intake air leak..