Forgive me if this has been discussed previously. GWMT is giving very strange internal link results. I've tried to ignore this as long as possible (just chalking it up to delayed reports etc) but its been several months now and I'm almost certain the bizarre internal link view is actually being reflected in the search results. Basically there are more internal links pointing to pages listed in the main nav than the home page or root domain! It appears as though on about 50 pages or so Google has ignored links back to the home page which IMHO could be significant. I'm using a template so every page should link back to root in the same manner site wide. This happen to any of you? What fixes it?
I have been seeing this for years. The internal backlink counts are just very odd, with many being ignored. They change in odd ways from week to week, even though nothing on the site has changed in that time.