Well, to anybody else who has had this problem (see early posts) and, perhaps, kept quiet about it - it has been completely fixed in the update to Thunderbird 17.0
They certainly took their time over it!
Junk handling has returned to its original, exemplary, self and the account settings now change when I want them to.
Thank you all for your help all of those months ago. Somebody at Mozilla must have been paying attention, even if they didn't let on.