Dr Pete, based on your questions, it looks like our website has been hit by Penguin 2.0.
"(1) Did the drop happen right on May 22 (Penguin 2.0) or earlier/later? Right on May 22
(2) I see a solid loss in the top 3 - which specific keywords were these, and do they have any commonalities (branded vs. non-brand, for example)? Loss in traffic (40%) exactly after May 22nd and rankings dropped for both branded and non branded keywords anywhere from 1 to 17 positions.
(3) Were these keywords all ranking for the same page? Was it your home-page or a deeper page (it's possible this impacted a specific page or set of pages)? Pretty much, 90% of them were ranking for the Homepage but all the inner pages have been affected.
No manual penalty or warnings in GWT, pages are indexed/cached and loading normal.