I have a look a the site and it is indeed an interresting puzzle:
Most of the pages have either PR5 or PR6. However, the index.html is only PR5.
There are not many pages on this site (about 20) and most of them can be reached directly from each other. Because of this 'nearly flat' structure, PR is probably similar for most of the pages, i.e. PR is either a high PR5 or a low PR6.
I compare two PR6 pages with the index page to find reasons for this phenomenon.
- There are backlinks from all pages to the index page (as far as I could see)
- Nearly all of the incoming links are to the index page. For one of the two PR6 pages which I have examined, I found an additional PR4 incoming link. However, the other PR6 page has none.
- Google considers www.domain.com and www.domain.com/index.html as the same page. Thus, a split of PR is not an explanation.
- The number of links on the pages seems to be also not the solution. For one of the PR6 pages exists more than one backlink on the pages (which could explain higher (transferred) PR for this page), however, the other PR6 page has just one backlink on each other page (as far as I have found so far)
Therefore, one has to look for other explanations.
If the structure of the pages is unchanges for the last 2 month, i.e. since the deep crawl before the last update (WebManager, can you confirm this?), then it seems that PR calculation is treated differently than in the original algorithm. For example, one can think of:
- graphik links doesn't count the same a text links (the backlink to the homepage is a graphic link)
- transferred PR depends on the position of the link
- link within the navigation template doesn't count the same as other links
Of course, this is speculation, but I haven't found a better explanation so far. (I will examine this site in more detail the next days.)
do you want to change the structure in such a way that the homepage is a PR6 page? Independent from the reason for the actual distribution of PR, you can change it. However, you can change the distribution, but the total PR (sum over all pages) will be unchanged. Thus increasing the PR for your homepage will decease some other pages. However, if your homepage is more important in your eyes (and also because Google seems to favour homepages in the results) you should do this.