They rise. But just to the tops of the muffin papers, not like a large dome.
I don't think it gets much better than that with whole grain flour. Mine rise about 1 cm above the top of the muffin tin, sometimes. If you want that large dome, I think you will need to add white flour.
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Without the recipe, it is hard to pinpoint what might to be tweaked. Also, the technique re: how the ingredients are blended would help. I sometimes add seltzer to things, in addition to baking soda/powder.