I never saw a pattern of Google listing the site: URLs in any particular order - and I really wanted it to be that way. On some sites, in fact, it does looks sort of like that. I was just looking at some site: results for a client earlier today and there was no relationship to PR or trust or traffic - the order was pretty borked to my eye.
The one thing you can sort of depend on is that the domain root should be #1 - if it isn't, something is wrong somewhere. But what that may be (your problem or Google's) is not always clear. The only thing that is clear to me is that it is not a healthy sign.