For me this problem went away when I upgraded to 0810.
The problem wasn't that autofs was mounting and unmounting the drives. It was that once an MD was booted up my media drives (SATA in the core) was were unmounted and never re-mounted, then when Updatemedia ran it could only find the same amount of media that was stored on the OS drive.
By using this idea to keeping them from unmounting I could boot up an MD with and still access my media.