Just a guess, but it's likely that some links have to be updated. I guess the fast startup speed we see in Jaguar (and other operating systems) stem from the fact that the OS 'knows' from the last time what will happen. (Doesn't sound very technical, but I hope you know what I mean.)
Now after a system update - or maybe if you changed some system files by hand - the OS notices that its expectations fail and first has to look for things it otherwise would find in the expected places (I don't mean files, I mean places *in* files).