Following up on the "limp flipper" issue: CGC said that the power coil automatically cuts out after 20ms (the internet says 40ms, so maybe that was a typo in their reply), and that this matches the behavior of the original Fliptronics II hardware. I.e., the EOS switches are a backup only, unlike with pre-fliptronics boards. I either never knew this, or knew it and forgot it. Hence the "finger test" behavior I described.
I'm pretty sure the problem isn't misadjusted EOS switches - they look plenty wide, and don't contact until very near the actual end of stroke.
Anyway, I've got a ticket open with them - but being such an intermittent issue, and one that's hard to observe when you're not playing, I'm not sure how I'll narrow it down.
w.r.t. the MMr flipper issue I'd made vague reference to: "I believe the issue you referenced with the Medieval Madness flippers was someone on pinside thought they found a variance in flipper timing that we introduced. However, the flipper variance existed on the original as well, as it only polls the flipper switches every 4ms, meaning on both the Medieval Madness remake and original, there can be a 0-4ms delay in the flipper firing."