I haven't studied the Newsletter Subscribe mod in great detail ... only enough to know that part of its implementation is a change in how the data is stored related to customer subscriptions. I believe the installation of the mod walks you through migrating existing data into the new format, and then the new structure updates the queries used to extract the data for purposes of mailing or exporting etc.

You could check the raw data in your "subscribers" table vs the "customers" table to see whether all the "customers" records where the "newsletter" field is set to "1" ... are also in the "subscribers" table.