2006 E53 X5 4.4i Automatic

I am getting codes:
54C4 VTG Calibration
5F39 Calibration Faulty

I cannot make get these to clear and stay cleared. These came up when my wife got a flat tire, or shortly after. We were on here spare for about 5 weeks. It is the factory 17" spare, the car has the factory size 19's on it.

No other codes. The gear in the transfer case motor looks like new, I had replaced it about 2 years ago. Transfer case fluid was changed last year with BMW DTF-1 Transfer Box Oil.

SAS is good, it is calibrated and reading good on the scanner. I am using a Foxwell 530 to read and clear codes.

Any thoughts where I should look next? How do I tell if the VTG module is functional, and how do I tell if the VTG motor is still working?