I think at this point, more than anything, I'm just taking away questions so that I can put this more firmly in SageTV's court.

In an unrelated search I stumbled upon someone else in their forums having some recent (similar) issues with their recordings, claiming also that recording with the native capture card's app didn't cause the problems. But it's the only thread I've located about it, so it doesn't appear to be a widespread (and therefore easy to test) problem.