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When I backlink some websites at their index.html pages I notice that Google reports links which refer to complex dynamic sub pages.
It seems like these complex dynamic sub pages are contributing to the PR of the home page or do you think they are redirecting the Googlebot?
Have your customers link to your homepage, yoursite.com/index.php or whatever. Just make sure the default index page is dynamic. Then your dynamic page can look at the referring URL. If the referrer is one of your customers links, then display whatever you're supposed to display when you get a link in from that person, otherwise display your home page.
I use this method to make sure people are reciprocal linking to me. My index.php page just checks where they came from, and activates their reciprocal link if I get a click from there page. No referrals, they never show up on my links page.