I am running BB V0.4. Earlier I was installing a theme through clockwork. The theme.zip was successfully installed, but I then accidentally applied "update.zip" from the menu that was there. I then noticed anything requiring superuser permissions to become unresponsive...such as ROM manager and the superuser permission application itself.
My question is, when the next version of BB comes out, should I still be able to install the ROM and the superuser permissions be fixed? Or is there a way this needs to be fixed? If it will work itself out then I wont worry. I originally rooted using the first droidmod updater (which I think was 2.0.1?).