adder - 10:06 am on Jun 23, 2012 (gmt 0)

But are you sure the drop coincides with the date for Penguin?

The webmaster says that it does coincide but he's being awkward and not letting me look at his Analytics :)

Why did some sites get the warning but others didn't?

I think you can get the algo penalty for an on-site over-optimisation too, even though your link profile isn't spammy. I've got a feeling that's what happened to one of my own sites. I never received a GWT warning (because all my links are super-good and natural) but I still got hit by Penguin.

if a site has 100 inbound links and 95 of those come from one site (say, a site-wide footer link) with the same anchor, could that disrupt the link profile?

Sounds like a recipe for a disaster to me. 95% of inbound links coming from a single site, I cannot see how that's natural :) I wouldn't pursue ANY sitewide links before my link profile is well established and strong.