%DATE% "Date of last modification" is actually the date the file was uploaded. [I might recommend rephrasing that in your plugin. But, to the question...]
Therefore, if the file is updated in any other way, for example, we use "Enable Media Replace" to easily update media/documents/attachments, the %DATE% remains the upload date, and not the file modified date.
Feature request to have that file date modified added to the options. And thanks.
The way around, of course, is to re-upload the file, but then its ID will change, and any references to it (and there are plenty on the site), will disappear.
EG-Attachments: Essential for WordPress as CMS!