Well, for what it's worth:
I activate the yeast first, ie get it started, with a bit of sugar and some warm water.
I don't knead the second time, just 'knock it down', possible a couple of light kneads to distribute the gases. 
Also, even a bit of added flour for kneading can make it too dry, which limits rising. 
It's all trial and error, not suggesting these will work, just things to try.