Same trouble here too. It's intermittent at high speed, and independent of all climate control adjustments (sorry PDFOOT). As frustrated as I feel about spending 30K for an annoying whistle, your situation sounds untenable. There is clearly a design/QC issue here, and MINI should address it.

Sooooooooooo, I'm off to check seals and block holes. So glad I bought a new car (my First! GOOD JOB!!!) I'm debating trading this car in for a 2010 Golf Diesel. My wife's Beetle sure doesn't whistle. The MINI could be a perfect car, if only the quality were a little higher, the rear view mirror way smaller, the dash controls a bit simpler and a spare tire. Otherwise, the car is AWESOME. Man, am I frustrated.
GOOD LUCK GUYS.

 

Mine ultimately proved to be a very small crack / nick in the windshield, behind the mirror / sensor. New windshield, no more whistle.

 

most whistles i ever encounter in a car is from the throttle body. The edges of the butterfly are too sharp causing a slight whistle under part throttle. the solution is to remove the butterfly and lightly sand the edges. I have this problem now with my mini and i plan to pull the TB soon to fix it.

 

Two Birds, one Stone! A second issue I have is the HUGE rear view mirror blocking my view, especially on right turns. I removed the mirror, dismantled and removed the electronic sensor for the Comfort access, reattached the sensor to the wiring and tucked it up behind the headliner - Viola! problem solved, remote works. During my test drive (how huge the windshield appears!!) I heard that damn whistling crap again. Since the mirror is now gone, I easily placed my fingertips at the top center of the windshield and pressed. The whistle IMMEDIATELY stopped. It started again as soon as I removed the outward pressure. I was playing a 75 mph tune alternating pressure on the shield. It ONLY took two months to pinpoint it. So suddenly I can SEE clearly in peace and QUIET at speed. I'll soon call the dealer to have the shield properly sealed. Suddenly, my two biggest thorns are cured and the car is now a keeper. Maybe I'll look for a windshield mount mirror I can affix to the BOTTOM center of the glass- we'll see.

 

Shield resealed, problem solved.