Robert_Charlton - 11:25 pm on Dec 9, 2010 (gmt 0)
Sites are all reasonably shallow linked (not too many clicks to each page)...
Not necessarily a good thing... This suggests to me that, in order to get the shallow or flat structure, you might have built some very large pages with a huge number of nav links on them. This might result in a miniscule amount of link juice available for each nav link.
Do you have a lot of nav links on a page or not? How many?
Directly related to this is what kind of inbound links you have. What is the inbound link quality like? Though a few comments have been made about getting good links and links to deep pages, I'm not seeing any response on this topic. IMO, it's probably the core issue.