It's not clear what you're talking about with the docking system thing. If your unrar disk is offline when Newsbin tries to unrar then of course you're going to get stalled downloads. Newsbin assumes the disks are there and functioning. It makes no effort to recover from something like a missing disk.
Would it be possible to map that setting to a toggle on the Status Bar? It's easy to forget to dig down and toggle the setting. It must have succeeded unraring in the download folder on the system disk a number of times. If it failed every time the USB dock disk was not assigned to a drive letter then I would have noticed it. Strange.
The reason I target to that drive is I have a USB 3.0 card and WD Caviar Black 6 Gb/s drive in the dock. It's faster than my 3 Gb/s system disk. But my set top box is not networked. So sometimes I pull the drive to watch videos that are on it(it's a WD HDTV for USB set top box.) If a status bar toggle is a hassle I'm sure I can come up with some macro to do it with a hotkey. But it would take some digging with a window spy to get the control names to artificially click the mouse etc..
edit: I've done 1/2 dozen downloads and the automatic unrar has worked on all when the USB dock is the target. Guess the simpler solution is just to stick another drive in the dock that has the same target folder. So far so good.