If I recall correctly the softkey assignments are saved with the scenes. Have you made sure that the assignments are correctly saved in each of the scenes?
Yes the soft keys settings are stored in each scene. Probably the cause of your problems but not a bug as such. Recall a scene where they are correct then you could make them scene safe and then update each scene.
Cheers
Richard Howey
Audio Dynamite Ltd
IDR48/IDR16/T112/R72/Mixpad,Tweak,
Dual M-Dante/DVS, 17"MBP/Logic 9/Custom Mackie Control