That is an extraordinary length of time. Leopard does take longer than Tiger to do Permissions but the most I've heard is about an hour, usually from 5-20 minutes is average on a lot of applications. Remember it only runs comparisons on Apple or third party installs that use the Apple installer method, that is, ones that leave a pkg with files to compare.
Lot's of other programs running could slow things down but not that much.
Have you done a directory update recently? (Disk Warrior) That might make a difference.
