Maybe, maybe not.
What I mean by that, is that this is how they came out after my initial pre-processing, aligning and stacking.
My procedure from here then includes wavelet processing in registax, deconvolution in AstraImage, recombine into RGB in AstraImage, and then further post-processing in Photoshop.
So when recombining into an RGB image, that's where I check the RGB alignment. It's likely that 1 or 2 channels may need to be moved by a pixel or 2.
It's worth noting that because of the long focal length, and the long capture time (40s each channel), some features have rotated between the Red channel and the Blue channel.
So when aligning the channels, if you align on the "edge/limb" of Jupiter, the features in the middle won't be quite aligned. I always align on the features themselves, which sometimes leaves a blue rim on the right hand side but it's more important (to me) that the features are aligned and accurate.
If you use the "channels" tab in Photoshop (once it's an RGB image), you can alternatively click on each of the Red, Green and Blue channel layers and look for any movement in a particular feature (eg: a white spot, Red Jr etc), and use the Move Tool to re-align each channel.
Hope that helps.