It is unlikely, but to eliminate database corruption possibility.
Make a copy of not opened database using duplicate in the OS
Open the copy and SAVE AS Smaller, test the import.
The new database has the same tables and field names?
Okay, I'll give that a try and get back... stay tuned.
This may happen if the target table has validation rules that are set to be applied “always” (i.e. not just during data entry) and the incoming data doesn't match these rules.
OS 10.6.2 and FMP 11.
I had a similar problem, importing from an xml file (iTunes library) with an xsl type sheet.
It worked perfectly, but when I tried to repeat it recently 40% of the 25.000 records were skipped.
I had been told to set the validation of a particular variable to "always", which I had taken as an absolute precondition for the success of the import of the records.
But your comment gave me an idea, and indeed, after setting the validation to "during data entry only" all records were imported.
So give it a try.