Based on the scenario you describe, most likely the files have a different heading ( causing a different hash value ) or the duplicate file check is not going enough cycles back to notice the prior input.
Assure builds a hash for the file, which is then compared to detect a duplicate ( so the files need to be identical ). If the file has a header with a date in it, and the file from yesterday / today have different dates, then regardless of the records being identical we would still see it as a different file due to the hash values being different.
One good resource to troubleshoot this type of issue would be the following page :
Within this "capture source list" page you may filter for the control entity, control point and source. Looking at the stored hash signatures over time will allow better diagnosis of why this may be happening. Please note, this page requires "superuser" permissions to access.