Thanks for the input guys.
I've popped the files into Besweet (well, Belight anyway!) ESB was rejected for some reason ("Error 32: No input-data was found (wrong substream?)"), but RotJ seems happier. (EDIT: I re-extracted the RAR and it works fine now, so please disregard that part!)
However, there are only two output modes - stereo or 5.1. I'm guessing the stereo will discard (or downmix) the LFE, and the 5.1 will be just, well, wrong?
I imagine the problem with direct encoding is that 2.1 isn't widely supported as a typical input (or output) format...