A very interesting and slightly strange change has recently been hapening with google pagerank. A large number of sites (including this one) have begun showing a lower page rank on the homepage then on the subsequent pages. Now occationaly this is caused by a larger number of links pointing directly to internal pages and bypassing the homepage, but in 99% of people's cases, the majority of their links point to their homepage or index page, so by the very definition of pagerank, the homepage should have the highest PR number. Recently this has changed though. Sites with absolutley 0 links to the internal pages are showing higher pr numbers then their index page. Why?
A lot of the major SEO forums including SEW, digital point, and webmaster world are full of people asking this exact same question and a number of different theories have arisen. I believe it to be this: Google initially calculates pagerank on the index page and then passes this on to all subsequent pages of the site. Then (for reaosns I'll get into) it applies a penalty to the index and/or other pages of the site. Some of the internal pages must have not triggered this penalty and/or filter, so they maintain the higher pagerank.
What penalty or filter did the index page trigger?
I'm not completely sure, but I believe it has to do with large amounts of non-relavent links both to and from the targeted site. There is a strong amount of evidence that Google's is penalizing pages and/or sites that contain links to pages that not on topic or considered relevant to their site. I believe this is to try and crack down on paid or bought links and other forms of articifical link manipulation. If you read matt cutts (google engineer's blog) he talks a lot about google's efforts in this direction.
What to do about it?
For now go through all the text and every link on your site. Any page containing a link to a page that is off topic and that google would not consider relevent add rel="no" to the link tag. On your reciprical linking campagins, try harder to trade with sites that are on topic with yours. Hopefully more experimental evidence will make it's way out there shortly. See the following links:
http://forums.searchenginewatch.com/showthread.php?t=10917
http://forums.searchenginewatch.com/showthread.php?t=11108
http://forums.searchenginewatch.com/showthread.php?t=10914
