The secondary signals we are used to seeing from Google have certainly shifted and I expect them to shift some more. As long as traffic stays healthy, I'm not sweating the side issues right now.
I think there's still a lot of "broken pipes" on Google's back end reporting, probably due to changes Caffeine introduced, and I expect to see those plumbing problems shake out pretty well over the coming weeks.
None of that addresses the situation where you also lost rankings - and especially traffic, since rankings now flit around like butterflies. I'd say that the jury is still out on this, but it seems to be, usually, a side effect of the Mayday update - and that's not 100% understood yet in the webmaster community.
What we can see is that, rightly or wrongly, the new algorithm has selected those pages as not being the best in quality for a search user. Google is taking aim at content farms, micro-sites and all manner of not-so-valuable content that used to rank well (and those sites still do in some cases). So the question I'd ask is what is it about these pages that looks off to the algorithm, even if the pages are high quality.
Ongoing discussions in the
Google Updates and SERP Changes thread [webmasterworld.com] may be of value to you.