i am running a Bama 93 race tune on my car, but i have not noticed the fan running all the time. it may be that way, but i have not noticed. my car has been garaged for over a month, so when i get it back out i will definitely pay attention to the fan. i am not running their CAI tune though... i just have the race tune with a K&N drop in filter.
Like I said if it wasnt so cold I probably wouldnt have noticed, in the summer the AC is always on so the fan is going so the fan running doesnt stand out much. I doubt the CAI has much to do with the fan, it could also be something they started doing recently as well. It does it will all three tunes, even the street.
The SCT tune does what I would expect the fan to do trying to lower the temp with a stock thermostat, the low speed easily keeps it at 195 when its cool out and the fan doesnt kick on until it warms up some.