BOAC, in the company I fly with any approach using VNAV/LNAV (and similarly on the Airbus using "managed") must be backed up by the "raw data". If the raw data shows differing information then the raw data should be followed. This obviously assumes all the raw date aids are available and coding correctly.
One for 100% on the Airbus - if the approach is in the FMGS database can you not fly the vertical profile in managed mode rather than FPA?