Rebel had the same problem, low sperm count with some missing heads or tails. Repro vet stated cause was stress. We took him out of training for several months, put him on Omega 3-6-9 and when he went back for another sperm count, they were all normal, complete with heads and tails, swimming all in the right direction and about 90 - 95% motility.
This is an interesting thread...helpful to me for my older boy. He does get hip/joint supplement plus oils, however not the same makers so may try switching.
http://www.midwoof.com/store/reprodu.../prod_222.html I think Myra Savant Harris also talks about this in her repro seminars.
Lee's threads always offer a wealth of helpful information when it comes to stud dogs.