Until recently my system has always been as bulletproof as humanly possible. A crash every once in a while but definitely not an everyday occurrence. I have always tried to take good care of it by flushing the P ram regularly, and repairing my disk permissions often as well.
2.66 Quad Core Intel Xeon
Mac OSX 10.6.7
AJA Kona LHe Card
Final Cut Pro 7.0.3
After I started getting multiple crashes each dayI tried to repair the disk permissions and got an error message:
warning: suid file "system/library/coreservices/remotemanagement/ardagent.app/contents/macos/ardagent" has been modified and will not be repaired.
ARDagent has always given that message, as it should. Remote Desktop has its own set of permissions which are not alterable by DU. You probably never noticed because it was hidden among all the other repair messages. It does not prevent further permissions repair in any way. That doesn't solve your problem, though.
You don't mention DiskWarrior in your post, which is probably the most important tool to keeping a sleek system. DW should be run whenever the system acts up a bit, or on any maintenance schedule you run. It corrects errors in the databases that DU can't. It also has S.M.A.R.T. and permissions repair utilities so you can do all your disk checking in one place. DW must be run from another boot drive to work but comes with its own bootable DVD.