Thanks for following me to the new thread, DK. That was sweet of you.
The domain for all the directories and pages is the same. The site is 15 years old, so we've gathered up quite a few links to www.example.com. However, we now use example.com as our canonical form.
Basically, since Google sees the www and non-www links as two separate pages, I'm afraid that we're not getting the benefit of those many thousands of links in, and may even have been penalized. The 301 redirect seems to be the preferred method for dealing with this issue.
The content within the head of the webpages is the same for the pages that are redirecting properly, and the ones that aren't. I've also now found some pages within the problematic directory that are redirecting properly, but there are very few of them. So this is problem is hard to pin down.
I'm going to send you a private message with some sample links, to see if you can figure out anything. If you don't want to mess with it, just ignore the message. Thanks!