This is a standard frustration point with new BMW owners, and some older BMW owners.

First, set the thumb wheel to the centre position, no red or blue dots.

Now the temperature setting on the HVAC will work just fine, and hold a different temperature left or right. Use fully automatic for the vents to be blended by the system automatically, or select one or more vent priorities (def/centre/floor) if you like, still using automatic fan control.

Understand that the centre vent control (thumb wheel) is not an absolute temperature control, it is an offset control. The three dots (red or blue) correspond to a 1, 2, or 3 degree offset from your automatic setting. That mixing only applies to the centre vents, it doesn't affect the outer face level vents.

As an example (using Celcius), I set the left to 19, the right to 20, and the offset to one blue dot, meaning that I get slightly cooler fresh air at face level, which is great for staying alert on a long drive.

The problem happens when people dial the thumbwheel all the way hot or cold, at which point it ends up fighting the automatic control at some settings. The system then can't deal with extremes of cooling the lower level of the cabin and heating the upper level, or vice versa, and resolve what you actually wanted in the first place.

So, leave the thumbwheel in the centre, and resist the urge to play with it for a few days. Do not ever consider it a temperature setting. But once you know what you want the main cabin temperature held at, use it judiciously to adjust for cooler or warmer air on the face vents, depending on your preference. One or two dots is usually plenty. And if the driver or passenger want different results from that centre vent stack, they can be independently shut off, just relying on the outer face level vents.

I had my system adjusted so that I kept the same temperature setting left and right all year, and adjusted the vents from one dot to two, and back, spring and fall. It worked perfectly.

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2007 X3 3.0si, 6 MT, Premium, White

Retired:
2008 535i, 6 MT, M Sport, Premium, Space Grey
2003 X5 3.0 Steptronic, Premium, Titanium Silver
2002 325xi 5 MT, Steel Grey
2004 Z4 3.0 Premium, Sport, SMG, Maldives Blue