The system never goes through a "permissions correction process" upon boot -- the delay you experience upon boot sometimes is the system performing a drive integrity check (fsck, to be exact). It checks that the relative health of the filesystem is good, but does no permission checking/repairing.During the forced power reboot, the laptop does not seem to go through a permissions correction process (ie; the long delay that you experience during gray apple screen start-up.)
If you create a new user account and log in under the new user account, do you experience the same freezes? If so, then the problem is likely with your general OS X install (meaning not specific to a certain user account), or it could be hardware-related (RAM, bad blocks on the HD, etc.). If not, though, then hooray! The problem is likely a rogue issue that is specific to your user account, which can be remedied with a lot less effort than a universal problem.