Problem with calibrating a PT100
Provisionally.

It seems that the dry-well block, which is a drilled Aluminium cylinder, cannot take our small PT100 deep enough. I used one of the larger holes, designed to take a large diameter reference probe, and dropped the PT100 all the way in. The results match what I expect much more closely. 

So, the answer is to have our own custom dry-well insert made to match the dimensions of the PT100s we are using