Well, the Summary says it all. When I was just having the root of /mnt see everything, most of the media was discovered on one hard drive. One drive was completely ignored by the Media server.
I am using a Rosewill drive enclosure that lets me use two hard disks to one USB connection. They don't show up as one big drive (like RAID), just individual drives. Pretty nifty setup. Just browsing, writing and reading, I can see files, including media just fine. Just when I use the Media Server they don't show up at all. I set them up as shares just like I did in the Samba File Share Setup page.