I was about to spend some time researching this, but realized someone might have already looked into it; if not, I may just answer my own question in a few hours.
Scid is pegging one core of the CPU, possibly trying to keep up with input from Stockfish? Stockfish is using 0% CPU, possibly blocking while piping output to Scid. That is just what I suspect is happening--haven't confirmed. In any case, stockfish takes a minute or two to get to 2 depth in analysis--usually after a few seconds I'm to 15 depth at least, so it's orders of magnitude slower.
I didn't change any of my UCI settings, just simply upgraded the executable. Same thing happens on Mac and Windows, so it's probably not platform specific, but something related to the UCI interface?
I have hash size set to 1024MB, "use sleeping threads" = true, and multiple variations set quite high (100 or so), to see all variations scored and searched, which helps in analysis even though it slows down the depth search. The rest of the settings are default (I'm fairly certain).