My experience is that comes from not letting it rise enough... so it might be a bread machine problem. smaller batch perhaps?

I would suggest that its not the yeast probably partially the amount of time you are letting it proof and probably the temperature you recipe calls for is too low, and last but the most likely issue is one of structure, Whole Wheat flour simply lacks by weight the same gluten content as white flour. This lack of gluten causes a weaker structure, less gluten strands and therefore it simply can not handle the gas buildup that regular white or bread flour can. ie no way for the fluff to stay in. You can correct this by simply adding supplemental gluten and/or reducing some of the not glutenous binders (I do both when making whole wheat bread) adding gluten is a simple matter, add a tablespoon of gluten powder to your WW flour at the beginning and proceed as you normally would. Their are also other things present in WW flour that prevent the formation of the gluten, a small amount of natural fat, an array of proteins to mention a few, these can be reduced in efficacy with acid, a little cider vinegar does wonders, a teaspoon should really help, You may also want to add a touch of blackstrap molasses or malt syrup these are both awesome food sources for yeast in WW bread. Finally I would reccomend raising your initial oven temperature higher, your recipe probably says something along the lines of 350°, bare minimum I bake all breads at 425° and most I bake at 550°, I use higher temps to get maximum gas production out of the yeast in as short a period of time before the starches in the flour can fully gelatinize causing your bread to "set" as it were no allowing it to rise any further.

my reccomendations come from both being a Cordon Bleu chef and also a former bakery owner and baker.

I simply use about 1/4 white "bread machine" flour... so you've got 3/4 wheat to 1/4 white... seems to work for me... also, it seems straight wheat flour need more moisture...

hope this helps and happy baking

:)
namaste'

All you need is some gluten, you can purchase at any store that carrys flour.

Thanks for all your advice...I'll keep referring back to it. Today I tried just reversing the white / wheat flour ratio to 2.25 C white / 1 C Wheat to see how that worked. Also, I just let the bread machine do the whole cycle to see what happens.