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Do these count towards PR?
Is there a way to get them to count? Do I need to re-word the links? Most go to a specific internal page, but that page shows no inbound links as well.
I've got 1120 pages listed in google that contain the term "www.mydomain.com", I have 0 that "link" to my site, even though there is a link to my site on all these pages.
You mean, they don't show up in a "link:" search?
Do these count towards PR?
If they are normal HTML links, they count towards your PR. Google simply doesn't display all links in a "link:" search. Only links from pages above a certain PR threshold, and only a selection of those.