Oh dear, I'm worried by the new and deep silence here!
Basically I'm back where I was - though at least that means that I've got my profile back! Thunderbird still ignores any changes I try to make to the individual junk settings.I have now unticked all of the boxes on the Options Junk handling screen and reset the junk learning process. These settings are holding but are having precisely no effect as even just now, when I looked before making this post, a new e-mail appeared and disappeared off to nowhere immediately.