Haha, thanks for the kind words Paul, and thanks for the help everyone else!
I decided to have a real try at getting some colour into my pics. Using a very short (less than 5 secs) avi I took the other night, I tested playing around with many of the controls in Registax. I made a short animated GIF with the results. Its quite small, but you should get the idea.
Next, I'll have to try with a proper large sized, long AVI of Jupiter and get some colour into it.
EDIT: I have finally found where all the colour in my Jupiter pictures has been going to. In Registax, after the stacking, waveletting processes, I decrease the brightness a bit to get rid of any blurry halo around the disk. When doing this, it darkens Jupiters cloud bands from brown to grey. I just tested this theory and its true. This explains why Saturn never lost its colour when I did the same thing to it. The loss of colour is now easy to fix - increase saturation and put the hue to the reddish/orangish area. Good as new.