My '07 had similar issues, started as an occasional taking over control, morphed into an every drive AC slams hard into defrost mode high speed fan, warmed air out defrost ducts and recovery only when system was put into manual mode, and then was slow to recover.
I did a system error scan with iCarly, it pointed to the windshield condensation sensor that is located in the inside mirror mount assembly. $150 in parts and 30 minutes of removing/replacing the plastic surround without breaking it, and all is good now.
Get access to a BMW specific error scan tool. It will she'd light on many of these aggrivating issues these interactive computers on wheels have.

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