The Site: search and Flow of PageRank

[purch]

It is my understanding that if I do a search for site:mydomain.com the results are like every other SERP in that the most authoritative pages are ranked higher.

So obviously I would expect my homepage to be first (in most cases), then followed by main category pages, etc.

My question is has anybody ever seen disturbing results when doing this (i.e. pages that should have no authority outranking main category pages)? Is this always an issue with site structure or can you think of other factors that may cause this?

[EGOL]

When I do a query like that I get "most relevant pages" returned.