In Lev Bishops 2003 article entitled "GPS Co-ordinate Transformations: an Overview" in Compass Point, the journal of the BCRA surveying group there is this on the second page.
Heights
Height datums are traditionally separate to horizontal datums for practical surveying reasons A distinction needs to be made between orthometric heights (heights relative to a geoid) and ellipsoid heights (heights relative to an ellipsoidal approximation to a geoid).
British OS uses orthometric heights relative to ODN (Ordnance Datum Newlyn).
GPS is relative to WGS-84 ellipsoid. Since geoids are irregular in shape, the geoid separation is not constant over wide areas. This makes conversion from local to global height references more difficult than the horizontal.
I am no surveyor and may well be wildly off the mark (surveying pun?) but it would suggest to me that you need to specify a height for your reference point as either a orthometric or ellipsoidal value and the programme processes the survey differently based on which datum you are using.
(All well explained in the link above from andrew)