I had this problem with my new Imac Intel of a long startup time. Perhaps it was related to tweaking the system with Mac Pilot 3, but I am not sure. The machine was starting normally, but then for many minutes I had a blue screen only and then the desktop appeared.
I used DiskWarrior with the new cd for Leopard I had made and now the startup time is normal, like it was before the problems started.
I really like this program which is way ahead of Disk Utility to solve problems like that.