As I did a brand new install (my policy) of Leopard, including permissions rebuilds, disk utility and DiskWarrior hard drive repairs, that would seem to rule out a preferences or permissions issue.
I always erase-and-install, too. The Software Update process introduces permissions problems, particularly on SetUID files that Disk Utility and DiskWarrior (v4.0) can't repair. Every Leopard clean install + Software Update I have done on Intel Macs has resulted in several (8-20) irreparable SUID warnings in Disk Utility, and takes a metric forever to finish. Apple says update 10.5.2 will fix these problems, but for now, rerunning 10.5.1 updater eliminates all but one of the SUID warnings.
How many SUID warnings did Disk Utility report for you, and how long did it take to repair permissions? If there was more than one SetUID warning, did you re-install the 10.5.1 Updater? Did DiskWarrior 4.1 fix all the SUID warnings? It only came out 5 days ago, so I haven't had a chance to try it yet. DiskWarrior 4.0 can't fix Leopard permissions, and isn't recommended for use with Leopard. (
http://www.alsoft.com/DiskWarrior/support.html )
As a Finder restart repairs it - it makes me wonder if this is, in fact, a Mac OS X bug. I will say that I keep PopChar, WeatherPop, and MS-Word running full-time - and one of those may be the culprit, I don't know.
Is PopChar version 3.3.2? Versions before 3.3.1 had Leopard-related problems. (
http://www.macility.com/products/popcharx/history.html )
WeatherPop (
http://weatherpop.com/?p=7 ) is reporting many Leopard-related problems. Commenters suggest switching to METEO freeware (
http://heat-meteo.sourceforge.net/ ).
Is MS-Word from Office for Mac 2008 (now available), or 2004? If 2004, I've had better luck on Leopard running NeoOffice freeware (
http://www.neooffice.org ) and Office 2007 in XP under Parallels (
http://parallels.com ).