The flaps in front of the engine are bypass for the radiator fan. unrelated to this question. The fresh air flaps are behind the cabin air filter which is in the engine bay at the firewall.

There is an F.Aux sensor next to the radiator fan that measures outdoor pollution and is one input in the auto mode for the recirculate function. They go bad after a decade or so, so perhaps yours is reading something that is forcing the system to stay in one mode or the other.

You should still be able to manually toggle between manual recirculate, manual fresh air, and auto.

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David.X5
2001 X5 4.4i Sport
SOLD! at 160k miles