Files uploaded to S3 using a 3rd-party uploader are not affected by the “Force Download” option in WP-Filebase Settings.
In your bucket manager, you have to change the metadata of the S3 objects to set the following HTTP headers:

Content-Type: application/octet-stream
Content-Disposition: attachment

Instructions using Bucket Explorer
http://www.bucketexplorer.com/documentation/amazon-s3–metadata-http-header-update-custom-metadata.html

And Using the AWS console:
http://www.techdreams.org/cloud-computing-2/amazon-s3-tips-quickly-addmodify-http-headers-to-all-files-recursively/5640-20110226