Forgive me if this is the wrong place for this, but I didn't see a general forum on techniques for shaping dough where this question might be more appropriate.

I tend to gravitate toward high rising doughs, since I mostly make sandwich breads for my family's consumption as sandwiches and toast. I have one recipe in particular we all like that's a wheat germ bread, calling for 4c bread flour, 2 c ww flour, 6 tbsp wheat germ and 3 tbsp flax seeds or sesame seeds, and 2 eggs (among other things). The proportions are pretty similar to most of the other breads we prefer, since we like whole grain or multi-grain breads.

However, I seem to have a consistent problem with this particular recipe, and have this problem enough with other recipes, and I'm wondering if my technique is off in the shaping or somewhere else. I'm getting big air bubbles, either right under the crust or sometimes elsewhere throughout the bread.

My usual technique is to knead, grease the dough ball and let rise until double, punch down, rest, divide into two balls, work each with my hands by folding the opposite way and squeezing out as much air as possible, working the dough pretty well with my hands until I have a suitable loaf shape, putting into greased loaf pans and letting rise again, then baking.

I'm thinking the problem is with my shaping process? But I suppose it's possible it's something about the way I'm baking. I usually preheat the oven with a rectangular stone on the bottom rack to 400 for 20 minutes, then bake for 30 minutes (or so, depending on the recipe).

Any ideas, questions or advice are welcome :)