there's a kind of decaying negative factor that spreads through the sites internal linking
Do you believe that added to that Google is being harder on the more competitive terms and verticals, or that it doesn't matter?
I'm thinking the relativity of the content with other sites may also play into it, since I'm seeing sites with great link profiles and content that stands OK, that have been busted. Maybe it's isolated within the site's personal poisoning as you say - the parent URL's i looked at did have about 30% poor quality pages linked to them and remained Panda'd. But those that surfaced in the last update were on child URL's where there wasn't a problem with the other child URL's and never produced much traffic anyway. Maybe the scoring also includes some consideration to folders - but I'd be careful playing with that, get it wrong and the whole site may be effected as you suggest. Just get the entire sites fixed and humming IMO
There has also been some suggestions by others that duplicate content overlapping from parent to child may cause a problem - but again i see some sites holding strong with that. It makes me think this algo has a long way to run before it's "stable".