I've looked a little further into the discrepancy between ConQuest searching and API searching. Once the difference between ConQuest and the API's notion of error is straightened out, ConQuest finds nine extra structures:
'BUDFEN', 'DENLOY', 'HOHKIA', 'HOHLEX', 'HOHLIB', 'IYEXUF', 'MURCIL', 'MURCOR', 'YAFRAY01'
These structures all contain 'Unknown' bond types between a Cu and an O, and so do not get selected by the API search. The structures will be found by the ConQuest search which, in the absence of a 3D parameter will perform a 2D search.
There is a good case to be made that a 2D search mode would be useful in the API. I shall raise this for consideration for the next API release.
In the meantime, if you want these structures, use ConQuest; if you can live without them continue to use the API.