Drall's situation looks interesting , especially with the cap on google referals.
But I'm concerned that there may be some confusion with issues that relate to a different type of Yo Yo where Google is confused or on the cusp of dishing out a penalty. The principle areas with my limited knowledge of where the Yo Yo can occur is in separate geo related Google data sets and a lack of authority ( lop sided link profiles being one aspect ) - which international geo region the links come from can be another.
My sense is that whilst Google's technology is ultra smart , the logic for consistancy with throttling is not there , and if it was it would be more widespread. I could be wrong , but that's how i see it.
Me thinks this is related to authority - but Drall certainly challenges that assumption.
Drall , on a large site like that you must have a lot of URL's Y/N ? Are they all cached and ranking with good link juice , or does the link juice kind of die in some areas of the site?
Did the new pages index and rank well when you added them ?