Upon further investigation, it appears that I caused this issue. I was trying to get rid of the subdirectory the torrent creator put all these files into, so that I could manage all that myself. renamed the top directory "\" rather than "/". Fixed that and the files automagically renamed themselves to the correct filenames. As for the directories. I believe the same thing happendd, but now they're full of special characters, and are harder to remove. A simple "Move Storage" command to something sane (after fixing the filenames in the torrent first, of course), moved the now-correctly-named files out of the troublesome directory and I could then use another "Move Storage" to put them where they were supposed to go.
*EDIT* with more info
Ultimately, I caused this issue. While the torrents were downloading, I specified the "move completed" option. The problem was that I performed a 'pwd' on my SSH client (puTTy), and then triple clicked to select the whole line, which I then pasted into the deluge GUI. Although it appeared correct, some special characters must have made it over. Selecting ONLY the text output of 'pwd' (instead of the whole line) results in correct operation.