I have a lot of trouble with Blue as well. Splitting into separate RGB channels prior to stacking as described in Mike's article http://www.iceinspace.com.au/index.p...63,306,0,0,1,0 helps a lot as you can apply different processing to the blue channel.
Next time, I'm going to try shooting a blue channel with a blue filter immediately after taking my main colour video. I guess I'm wondering if I focus on just the blue if I will get a better blue channel.