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Just out of curiosity ... have you removed/inspected/cleaned the Cabin Temperature Sensor?
There is a tiny fan in it, and it collects airborne dust, pet dander, etc. In "AUTO" mode, this sensor tells the CCU the current temp in the cabin. The CCU then configures the system to get you to the desired temp. If it cannot sense the correct cabin temp, it might result in the symptoms you describe.
When you place the temperature control to the "blue" position at 6:00 o'clock, you bypass all of that, which may account for your fan working only in that position.
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