Fixing permissions on your start up disk.

This isn't really a question but rather a comment/ query. Numerous people, when helping some one on this forum suggest/advise that you run a permissions check/repair from Disk Utility. I have done this many times, but just recently my Mac started to act up really badly, my Mail wasn't accessing my .Mac account, mirror agent wouldn't quit when i tried to log out, loads of nasty stuff. Then I noticed something I hadn't seen before. Something about repairing permissions on your startup disk. I followed the instructions, a lo, all is well. There were loads of permissions needing fixing on my startup disk.
I'm just a little disturbed. I thought that when I ran Disk Utility, it fixed all of this. So, where exactly were all these messed up permissions? Am i right in assuming that I was previously only fixing permissions in my account and not the system it self?

I've never come across any one mention this in any threads and I am surprised as it had a massive effect on my Mac.

That's all, just thought I'd mention in case anyone comes looking for help

"Repair Permission" can help establishing correct permissions to files and folder to various users/groups, but doing so could also cause unnecessary problems. Although repair permission was a standard practice under 10.0 & 10.1, in 10.4.x it is not desired for most users. It is also important to notice that the repair function works only for the packages which keeps a copy(.pkg) of permission references in /Library/Receipts folder. Rest of the apps. will remain untouched.

For more information please read this article.

Thansk for the reply.
I need to clarify something here.
According to Disk Utility, to repair permissions on your starup disk, you need to start up from you original OSX install disk, and use Disk utility from there. It is a whole different ball game than just normally doing it.
I've started to read this article and it claims you can do that normallly right from in Disk Utility as normal (not starting up form the install disk)

Just to re iteratte, this most recent pernissions clean up has completely turned my Mac around form something I was getting worried was on it's way out the door, to a brand spanking new beast...

Well in the Jaguar and Panther days this had to do with the BOM (Bill of Materials): as you used your Mac, the BOM got updated as time went on while the one one the restore disks never did. It was said to not be a good idea to use DiskUtility from the CD because it would compare the BOM on the CD and the one on the hard drive and it would replace the newer BOM with an older BOM.

Now I don't think this matters much with Tiger anymore because I think (but I could be wrong) that DiskUtility in Tiger works differently. Anyone can verify or contradict this? I wouldn't want to tell something that is wrong.

Oh and Sim if you want to get an idea of what are permissions exactly in the Unix and Mac OS X worlds, this might be of help: Mac OS X Unix Tutorial - Part 4 - Managing Permissions.