It might very well be that the whole wheat mixes create a tougher crust than you're used to...
We mostly stick to sourdough recipes (bags of mix) and simply follow the instructions.
These are premixed bags of ingredients...
One thing to note, the crusts on home made breads are (in my experience) significantly more rigid than those of "store bought" breads, and chewy or not, I really like the freshness and taste...
Keep playing with it (trying out different recipes), and you're likely to find one or ten that you enjoy.
Or get yourself an electric knife (or chain saw) and use the thougher breads as a side (instead of crackers) for soup!!