Have recently been through a situation where a mistake was made, not identical but similar and corrected within a week. Despite that, at least six weeks before something resembling normality returned, on a domain with an excellent link profile and regularly spidered.

Maybe Google are becoming a little slower at reversing change and the problem will solve itself, although there is one aspect of the set up that is a slight concern, the domain interlinking. I appreciate this has always been there but things change and this is an area where Google have been punitive recently. Whilst they accept that reasonable domain interlinking is okay, even where this has the potential to pass pagerank, the Inet set up could be just the wrong side of that. Small aspects, such as having main menu items also linked to one of the other domains have been felt by some to tip the balance.

I am not stating this is a problem but does warrant thought.