IF you are really sure that you don't have records with duplicate matches in your import source... (I'd double and triple check that one)...
Another thing to look out for: When you select "tables" for your import, you are really selecting table occurrences (boxes in Manage | Database | relatioships) If there is more than one table occurrence for your target table, it's possible to have a different found set for one Table Occurrence than found in another even though both refer to the same base (Data source) table. So it's possible in some situations to pull up a found set on a layout based on Table occurrence A, but then match to a completely different found set during the import if you either used a script to do the import and referred to table occurrence B or manually imported from a layout based on Table Occurrence B.
Oh wow! I would never have thought of that, but it sounds very plausible. Thank you so much!