Bryanna Clark Grogan, whose Gluten Free Yeast Bread recipe is listed in the Gluten Free section has discovered the key to making an all whole wheat loaf of bread in a bread machine. Please see her blog post for two fabulous recipes, as well as an explanation of why extra steps are needed to create a flavorful whole wheat loaf in a bread machine.
Making 100% whole wheat bread in a bread machine presents special challenges. As explained in the section on kneading, getting the flour/water proportion correct is done by feel, as opposed to measuring out ingredients in specific proportions. Different batches of flour have different moisture levels. Humidity levels also affect how much water needs to be added.
Bread Machines are designed to have an exact amount of each ingredient added in a specific order, and then have the machine operate un-attended to mix, knead, and bake the bread.
This works well with doughs made with some or all white flour, but not so well with 100% whole wheat flour. While I do not have a bread machine, I have worked with them at the homes of friends and have yet to produce a good loaf of all whole wheat bread from them.
Additionally, not all bread machines are designed for whole wheat breads, which need longer kneading times and rising times. From my research, the one brand which WILL work is the Zojirushi.
Even though the Zojirushi has the ability to do a longer knead cycle, and longer rising period, this still does not overcome the problem of developing an all whole wheat dough that has great texture and good flavor.
Do check out Bryanna's blog entry, listed above! Sounds like this is the key to great 100% Whole Wheat Bread in a bread machine.