Why is my bread not rising?

I've been using my bread machine and regular flour (just bought some bread flour tonight ... does it really make a difference?). I think the problem might be that I've been messing around with the recipes? For instance, I found a milk bread recipe I like but would rather use more wheat and not so much white flour, so I substituted. This last loaf actually came out pretty good; the three previous ones (one I messed with ingredients; two I followed the recipe) were quite dense and I could tell they just didn't rise like they should have. What is proofing in the pans, and does that happen in a bread machine? Would I be better off using the bread maching for the mixing/kneading, but then taking it out, putting it in my own pans, and baking in the oven? I'm still a novice here, but love making fresh bread for sandwiches and the like rather than buying it in a store. (I'm not quite there with the whole grinding my own flour yet though! )

Oh, and do you ever add ground flax seed (that I do)? If so, do you add it in addition to the flour or in place of the flour? (For instance, leave out 1/3 cup flour and add 1/3 cup ground flax seed instead.) I'd love to do that ...

ETA: Oh, it's usually 4 cups of yeast and 2 1/4 teaspoons of yeast for the recipes ... I tend to make 2 lb. loaves.

I hated how my bread machine baked the bread, so I always used it for kneeding. Bread flour does make a huge difference. In the States, but not in Canada. I use my mixmaster now and prefer it over the machine. I actually bought a machine and then returned it the next day. I find I can adjust the liquid/flour ratio. The mixture should not be dry or really wet. It should be a nice soft dough and depending on the flour, humidity and everything else the amount of flour needed can change day by day. Proofing is when you have punched it down from the first rise, shaped it and put it in the pans. You then let it rise again in the pans. You will have a dough setting on your machine if you want to bake it in the oven yourself. Do not mess with the ingredients or amounts with a breadmachine. You must follow the directions, ingredients and amounts to a T.

Why bread flour makes a difference: it is higher in gluten. Gluten is a sort of rubbery protein and when the yeast exhales as it dies in the oven, it blows up bubbles in the gluten. You can get whole grain high gluten flour. (Gluten is the stuff in wheat that most people with wheat allergies and sensitivities are allergic to, btw.)

How to know if you have kneaded the dough enough: take a small piece of dough and stretch it between your fingers in a square. If you can make a window that allows light through, you have kneaded enough. If your dough tears, knead it a little more.
Another test: when the dough feels as smooth as your earlobe, pull away a small amount of dough from the mass, and then let it spring back. If it springs back, you kneaded enough--if doesn't, you didn't. It is important to knead whole-grain bread dough long enough. It's possible to knead it too long with a mixer, but not by hand.

Also, don't add tons of flour in the kneading phase. The Laurel's Kitchen Bread book warns against this. If you think the dough is too dry, it's okay (if a bit tricky) to knead in more water.

How to know when the bread has risen enough: first rise, in a bowl--wet your finger and poke the dough. If it sighs and deflates, it has risen TOO LONG. If it fills in right away, it needs to rise longer. If you get a hole that only fills in very slowly, you are just right. You can do the same thing when you proof the loaves, though most recipes will tell you how high over the bread pans to let the loaves rise.