It's because not all people are linking to your homepage. For example: http://www.frum.org/ links to your inner page, not the homepage. It's nothing to worry about - completely normal.
because it's a "page" rank not a website rank...usally people have more backlink to the home page than sub pages...so that's why it's like that...but if u have lots of links to the sub pages, u get higher PR on them
Yes, if the links will be listed on the directories you have submitted. This is the probability of PR. Increase in link popularity = increase in PR.
I agree. I notice that sub pages have high PR because it has text content and outbound links on the page. But I'm not sure if outbound links is one of the elements that contribute to get PR on a page.