After using both for a good while now. I get frustrated that questions appear on the front page before they appear on the newest question list.
They should at least show the newest questions at the same rate.
I've noticed this as well. I originally thought How do you stop scripters from slamming your website hundreds of times a second? was asked by Jeff but only just discovered it was edited by him and asked by someone else.
The situation described in this question is a lot like the "Newest Questions" link. You could think of new questions as a resource people want to get early access to new questions. One way to deal with this (like in the question) is to aggressively cache it and it does seem that Newest Questions does at most update every minute or so.
The home page is probably cached as well but perhaps with a different refresh interval. If enough people cotton on you may find the home page getting slammed instead of the newest questions.
I agree it would make sense if they were consistent but it probably isn't the easiest thing to synchronize and the payoff is probably quite small so I'm not sure we'll see this anytime soon.
I never use the front page myself so I would never know if they shot up there faster than on the new questions list...but it may have something to do with the order that things are updated on the website behind the scenes, just a guess.
But overall I agree. New Questions ought to be as fast as possible. Make all my refreshes worth it.