According to yahoo auto, this car has a Motronic 7.2 system in it:
http://autos.yahoo.com/2001_bmw_5_series_540i_6_speed_sedan-features/

I tried to connect to my buddies car earlier with the latest version of the NefMoto flashing software.  Wouldn't connect in either slow mode or fast mode.  I was able to connect and read the flash from a 01 A6 with the same software/laptop/cable so I don't think there is a hardware issue.

I also tried the adaptation software (Unitronic) and it would not connect.  Saw the USB->Serial interface though.

Any ideas on what might be going on?