Thanks guys.
David, both
If a storm is present, then you should capture it like Jupiter - that is, shorter avi's so you don't "smear" the features.
However most people just capture for longer to get more frames = more frames to stack = smoother image with lower grain/noise.
I capture for 2 minutes on each channel, and an additional 2 minutes of luminance - though i'm not too happy with how the L channel is turning out. I don't know if it's blocking IR.
For Jupiter, it's 2 minutes MAX (all channels combined).