Hi BEBOP,
I'm sure you have tried all the above advise.
I was thinking that the only way to save your pedal assignments is to save them into a registration memory as Graham stated. I wanted to be sure of what I was going to suggest before I replied to your question. I fired up the 9000 and made specific pedal assignments and tried the panel settings save as others here have mentioned, then I shut the power off and restarted it. As I suspected the configuration of the pedals reverted back to the factory default of Sustain and Fast/Slow effect. Unless I'm doing it wrong...(don't think so) You must save in the registration banks.

Dennis