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Here is the issue. They are just not getting much in the way of organic traffic. I took a look at their site and the G toolbar gives it a PR0, which is kind of odd since they have been around for 6 years and have dozens and dozens of real links that they garnered not for PR but for actual traffic (imagine that) from info sites that relate to the product they sell. Google shows none of these links as backlinks. I can't imagine it's a penalty, since they just decided last week to take a look at their organic traffic and have done no SEO in the past.
They have two domains for the same site, but I don't have definate info on whether the non-advertised site is a redirect or a parked domain. It apprears to be a redirect though.
I told them to check their robots.txt. I also asked them to find out if the secondary domain is redirected or parked, as those can both cause issues.
What other reasons might be causing search engines (not just google) to avoid their site?
Do the backlinks that don't show up have PR of 4 or greater? Even if not, though, a PR0 on the home page is odd.
Did you compare the www and non-www versions of the site? I've seen a fair amount of weirdness caused by separate indexing in the last year or so. Check links and PR for both versions.
Check the server headers on the redirect and primary sites. It could be that Google thinks the redirect site is the "real" site instead of the one the client is trying to promote.