After enjoying many of the recipes out of The Bread Baker's Apprentice I moved on to Peter Reinhart's Whole Grain Breads to learn about how to make hearth-style 100% whole grain bread. Unfortunately my first loaf reminded me of the total flops I used to make before reading through BBA and using its recipes. It was like a bread brick. I ended up deciding that croutons were the only suitable use. Since then I've made more recipes from the book, but always using his "transitional" variant of half bread flour, half wheat flour. These have risen and proofed perfectly.
The technique from Whole Grain Breads involves pre-doughs. Flour, a very small amount of yeast, and water make up one dough ball that is placed in the refrigerator overnight. More flour, salt, and water are left as another dough ball on the counter overnight. Both enzyme activity and the rise in the fridge contribute to the texture and taste of the resulting bread, at least as far as I understand the theory. The next day the final dough is formed, allowed to rise once and proof once, and bake.
With my first loaf I attempted a free-standing boule. I know that surface tension is critical to getting a boule to rise up and not out, but I am pretty sure that my surface tension on the boule was correct. For the transitional loaves since I've used a loaf pan and a sandwich shape, which may have helped them to rise. I've also done transitional pitas which seemed to puff up just fine during rising, even during proofing as small boules before rolling out.
I don't want to try the 100% whole grain recipe again without knowing that it will work. I know that some bakers add vital wheat gluten to 100% whole grain recipes to ensure that they rise, but it seems like Reinhart's recipes should work without the additional gluten. Any other ideas for what may have gone wrong?