If this is happening just since you installed that tune, drive it awhile. 2 of my 3 Brenspeed tunes (CAI package deal) have required me to drive the thing almost a week before the computer can figure out how to deal with the new settings. I was busy trying to fix it myself and kept reinstalling the tunes, so I was starting fresh over and over, and it never got better. When I finally gave up and just drove it, it sorted itself out in about 5 days.
Dunno if that's the way it's supposed to work, but that's what it took with my car. Oddly, that one tune worked right from the start....?