Where did you get the recipe? I think Mollie Katzen has one in her Sunlight Cafe cookbooks, let me know if you want it. I will have to do some digging around, but we're cleaning today anyway so I should find it.
Don't have any recipies offhand to give you, but when I have made it I never use all whole wheat flour, just a portion...like if it calls for 2c flour I would use 1 1/2 wwh and 1/2 c white. I've never had a any problems. Also are your baking soda or powder effective or not too old?