tedster - 7:22 am on Jul 27, 2010 (gmt 0)
Major changes to internal navigation can trigger this sort of penalty as easily as suspicious back links and I suspect that in both cases the answer líes in the anchor text.
I almost overlooked your wise words, conor. I most definitely agree and suggest that curious take a good look at internal anchor text to see if it has unintentionally gone into warp drive instead of just doing what it needs to do. Google is no longer "hard of hearing" and can react poorly when a site yells at it too loudly.