Mapped drives won't show up in your backup view...I'm not sure how you're selecting those. I assume that you're selecting them through Entire Network, and then browsing for them.
When a backup or restore is run, the Media Server wil attempt to establish a connection to the Remote Agent running on the target machine. If this connection isn't established, we attempt to push data across the network, while not utilizing NDMP.
If you install the Remote Agent software, we establish that NDMP connection, and stream the data across the wire much more efficneitly. We also have timeout and retry functionality built in to the Remote Agent. That functionality isn't available if you don't use the Remote Agent.