I'd say you're right - there's been very little discussion of this particular update. In fact, only a few webmasters reported a change, but those that did seemed to feel a major impact.
I really doubt that this was just content or links. If it was, I think it would have been more widely noticed. However, impacting all your subdomains sounds very harsh to me.
Do you have any clues? Are you aware of any issues (past sins) that your site might have?