Its not a dish/alignment issue, as the beginning of the recording is fine, and the same channels are fine on my other HR20-100 and my HR21. Unless one of the ports on the MS is intermittent, this is a software problem.
The first time it was the MLB-EI recording, and the second time was the gymnastics on Sunday night.
I think that if this happens again, I may not be able to stop my wife from calling D* to cancel!