Please correct me if i am wrong...
If you put your phone into the stock holder in armrest then it is connected to the system trough wires and not bluetooth so it should work withouth pairing it to the car (this is the way benz phones work) so my guess is that your phone module is broken or some cable is loose or something

Did you try to reset the car by dissconecting the battery for a 30 min or so (i had some issues the other day after my batterie died half of the instrument cluster was not working, like RPM, Fuel, CheckControl and so on i called the dealer and he told me to do this to reset the car and it worked)

Just cal your local BMW shop and ask for help, they will charge you 500skr/hour ($80) to check

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X5 4,4i-06 Current
330Ci Cab-03 2007-2008
MB E55 AMG-03 2006-2007
Z3 2,8 Roadster-98 2006-2007
X3 2,0d-05 2005-2006
320d-99 1999-2005