Is the importing being done as part of the migration process? Have you tried exporting the records from the version 6 file into Filemaker format and then importing them manually into the converted FM11 file?
If, during an import, validation fails on any field, then the record won't be imported. Have you trapped for errors? Did you get any message at the end of your import saying some records weren't imported? Look at that table and see if there are any validations on any of the fields.
Also, are you importing just 'add' or are you mapping to key field and also updating?