Aah, that makes a difference
AS!3 is (by all accounts) much better than AS!2 so well worth upgrading to.
Registax has a very good Auto-RGB tool which works well for Jupiter (as there is a good colour range and some nice white points), I hope you don't mind but I have taken the liberty of taking one of your images (using a simple screen grab) and applying the auto-RGB tool in R6 to it (see attached). You may not notice the difference, but it looks better to me. Maybe it's a little pink, but you should be able to do better with the actual captured image, not just a screen grab from my monitor.
I have found that with my system, once I have found a good colour balance for my images (and the auto-RGB settings for Jupiter is a good start), I apply the same colour correction to all my images. So in your case, maybe a similar colour correction (r1.07 g0.95 b1.08) could be applied to the other planets as well. You could look at a number of your Jupiter images and see if they all give similar colour shift values and find a typical result.
I find it very difficult to combine different captures together in WJ, primarily due to the field rotation between sessions. Unless you align the images perfectly, the resulting de-rotated stack in WJ is worse, not better. I used to take 10000 frames (at 20fps under Backyard EOS) over about 8 minutes, link them together into 1 long video in PIPP, derotate in WJ (both field and planetary de-rotation) and stack the result in AS!3. It took a long time in WJ, and the result really wasn't much different from when I stacked 5000 frames directly in AS!3. You may have more success than me however ...
Hope this helps,
Andrew