Let's check the database directly. You'll need to get the submit_time key for the submission.
On the short code builder page, create a cfdb-table short code
- in "show" put "submit_time,UPLOAD_FIELD_NAME"
- then click the short code to see the results.
- copy the submit_time from one of the bad entries. It will be a number like 1363479099.2186
Then go to PhpMyAdmin, execute
SELECT * FROM
wp_cf7dbplugin_submitswhere submit_time = '1363479099.2186'
(using your submit time).
One of the rows returned will be for the upload field. In the "file" column, it should be something like "[BLOB - 21.8 KiB]", If it is "NULL" then it is empty.