If it was a manual penalty I presume I would have had a message in WMT?
Not necessarily. You get that kind of information often after you submit a Reconsideration Request. If your drop did not happen on a known Penguin/Panda date, it would be good to find something you can clean up and then submit one - just for the "manual/no-manual" feedback.
It does look suspiciously like a manual penalty. The other algorithm tweaks do not often have such a dramatic effect.