Especially in the case of imported data but also in case of incorrect manual entries, it is possible that there are in the fields non-visible elements such as spaces, which can affect the number of records found.
Have a look to the indices for those fields.
Thanks for the suggestion, but in my data clean-up I was pretty thorough. And now new insight has come to me.
Update: I now see why some of the metadata isn't showing up. My set up is
Specimen --> Sample --> PackedSample
So a packed sample has an fk_SampleID, and a Sample has an fk_SpecimenID. What is happening is that in the exported sheet, when a sample has been packed more than once, only the PackedSampleID shows up, and for some reason the duplicate fk_SampleID and fk_SpecimenID won't show up. They also won't show up in the found records. Knowing this, is there any way to fix it?
I suspect that you are searching records in one table using criteria specified for another and that your records export is exporting related data, which will produce incomplete rows of data in your export.
I can't tell that for sure from the incomplete info in this thread but that would fit the results that you describe here.