Hi Tosh,
After you enable your sidebar panels so you see "Alerts" , "Retain Search", "SameTime contacts" and "Sametime Primary contacts"...if you manually arrange them by dragging them up and down in the order you wish.
If you close Notes and open it again, are they in the same order they were in before you closed Notes.
Doing the above works fine for me (granted, my v9 Notes Client is on Windows but I'm not sure how that would make a difference).
Regards,
Paul.