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Is the site structure/internal linking scheme the same on both of the sites?
After inspecting backward links, I'd look very closely at the structure of the html. Is site A laden with html code (tables, graphics, etc.) right after the <body> tag? Does site B utilize css?
I'd have all sorts of questions in regards to the structure and internal linking. I have many sites that outrank higher PR sites that have more backwards links. Remember, PR is just one factor in the algo. It is a rather large one, but, there are other factors that could trump PR. That is easily confirmed by reading various posts here at WebmasterWorld.
site A utilize css, and site B doesn't utilize css.
keywords appear on the title tag, keyword tag and description tag for A.
keywords also appear on the first sentence of the body, and appear frequently with text word, image name, link name and image alt in the body for A.
A and B all use table.
Keywords of site B just appear in a paragraph including 3 sentences.