Try grinding up the flax seeds into a powder before using them. A good blender or coffee grinder works great. If you eat the seeds whole, they have a very hard shell that your body would have a very difficult time breaking down to get any nutritional value out of. If you grind up more than you can use at one time make sure that you refrigerate the leftover powder.
Ground flax seed is also great in protein drinks, on cottage cheese, mixed in with tuna and sprinkled on scrambled eggs.
-Jon