I think that one thing that probably causes a lot of confusion for most people is that the algorithm google uses to return search results is far more complex most likely than the algorithm they use in the Google Keyword Tool to return lists of keywords.

I've probably spent more than my share of time trying to wrap my head around this and it is the best theory i have come up with to date.

Also, i think that some of the ranking factors are significantly disproportionate in weight when comparing a regular search vs. a "phrase match" search.