Well for everyone who has been helping me through the saga.... I've done about every troubleshooting trick I've been able to come up with, replacing wires, switches, moving the server to eliminate the attic wire run. I turned off the bonded nic's. I can find no reason for this.
I'll rely on my last check. I used my 5 year old ASUS i3 laptop and plugged it into the same port / cable the Shield was plugged into. I installed PMP on the laptop and there were no issues streaming HD Audio and the original video format.
The more movies I watched pieces of, the more I'm seeing this sporadic freeze and jump on the video processing, seemingly at least some in every movie. It's only a fraction of a second but it goes from the barely preceptable to unacceptably bad. There is no timing pattern to these little "studders/judders" and the more that is going on in the scene the worse it is.
I even re-ripped one movie where the video wasn't compressed with handbrake and no change.
I can only see one of two things. I have a bad Shield or it just can't handle the bitrate of these videos. It seems hard to believe that this symptom could be bad hardware. However, based on everyone's feedback here with no issues, I'm going back to Best Buy tomorrow to have them swap the unit. I guess I'll know in a couple days.
Thanks for the help.