The way links are being used to rank sites has changed.
Its taking longer for them to be effective - if at all.
I think old existing links are still holding most of whatever power they had whilst still in place.
I think newly found links are being looked at differently.
I cant explain it - but I know its true.
I remember a couple of months ago some google engineer saying "we will be changing the way we handle links soon" - well - its happened I am certain.