Thanks Dtango & Snafu for your replies.
I read up on some past threads and eventually got it - yes, I see now that here are two parts to programming - the first being to allocate functions (B1,B2 etc) to your joystick buttons. That is what I was missing and was instead going straight to assigning flight functions to the stick.
It sounds as if you can use the advanced interface to sort it but that's too much black magic for me. I've done it thru the AH buttons.
Interestingly, there was a glitch when I had alocated buttons, and then assigned them to (in this case) Fire 1,2,3, but it did not work. After exiting the game and going back in later, it worked. Bizarre.
BTW, it is my first poper stick and I am blown away. SA has gone up 100% with the hat, and I feel I am competing more evenly with my opponents. I was on keyboard and mouse for ages!