I would recommend updating the plugin to remove the ability to upload via the "choose file" link in the next version of this plugin. As it is using an alternate uploader, it does not function in the correct workflow of WordPress.
For instance, for those who are using an alternate directory structure, the files uploaded do not conform to the topography. An example is anyone using Amazon Web Services. Using the standard media uploader, our files go to https://csdfjbsdb.cloudfront.net/directorystructure. But the upload mechanism for this plugin doesn't put the files there, resulting in them not being accessible in the media uploader at all.
I'd recommend removing the prompt and change the button from "Choose from Media Library" to simply "Media Library". That button allows you to choose or upload to the built-in wordpress media library, which removes the problem of duplicate media locations.