In version 1.7 of Moodle, there is an Advanced assignment type of multiple revisions think that you are looking for. It is correct that the assignment type single file upload, however, only allows a single file.
From looking at the code, it does not appear that the Advanced assignment type will be ported to 1.6 or earlier. But there are other multiple file types that you will find in this forum if you need it before your server is updated.