Did Google change the way related links work?

I've got a bit of a puzzler on my hands, on an established site that has never had this problem before. All articles use related links, usually embeded within the content or placed immediately after it.

As of late the wrong pages return for the search terms, example: Blue widget guide vs blue widget list. Both articles have a link to the other, both were highly ranked before (top 3) but now Google's returning the wrong page almost all of the time.

A search for "blue widget guide" returns the "blue widget list" page as most relevant for that term and vice versa. Worse is that since it's the wrong page it ranks extremely poorly.

I received a manual response to a reconsideration request stating there are no manual penalties so something else is at play. Could it be that if you write about something, and include a link to it, Google ranks the page being linked to more highly? If that's the case it would explain why all of my pages rank so poorly out of the blue. Besides Panda, what else could it be?