I have been making a lot of seed breads lately, and whilst hand kneading I have found that the seeds definately tend to cut the structure of the dough and potentially reduce the openness and rise.  I have taken to kneading seed breads less, folding more, and letting them have a long cool rise where the yeasts can do the work.

Two suggestions:

• Are the seeds dry or soaked?  If find it best to let the seeds soak for at least 4 hours, or overnight, in 150%-300% of their weight in water (if in a hurry, use use boiling water and let sit for 1 hour).  You might add a gram or two of the salt to prevent any fermentation or sprouting.  The soaked seeds are much softer and do less damage to the dough.
• After your machine finishes the kneading cycle, take it out of the bucket and shape it as if for a loaf pan (stretch, fold in thirds, and roll into a log a bit shorter than the machine bucket) except don't roll it as tight as you would if you were shaping a hearth loaf.  That redistributes the added stuff through the dough and also results in a nicer looking top surface.  (I also clean and oil the blades at that point so they won't stick when I take the bread out).

sPh

Thanks for the suggestion. When adding the soaked seeds do I press the excess water out or just drain the excess?

.....  BobL

Thanks. I'll try it.

1. lower the salt, it inhibits yeast growth, (I'd drop it to 1 tsp.) and 2, try some vital wheat gluten. Just follow the directions on the package.(4 tsp per loaf) I use the vital all the time with my bread machine, and I wouldn't make bread without it. I get a better spring, and especially with the wheat bread.