Why did so many permissions need to be repaired after Mavericks?

Here's my story regarding Repairng Permissions; its seems a repair is the only thing keeping my Mac running.
I've a Mac Book Pro 15" Spring 2011, been doing the upgrades etc ever since, but after Mavericks upgrade I was having issues never seen before with my Apple upgrades.  In short after upgrade I was getting gray screen, blue screen etc. Random screen splits with horizontal lines.
Took many tries to reboot, safe reboot, clear pram, etc.  I ran EtreCheck got rid of lots of things. I broke out disk and ran full hardware test - all good.  I have reinstalled OS X, as well as done two clean reinstalls of everything.  Even after that, I would still crash from time to time, with gray and blue screen either after re-awakening or simply opening iPhoto.
Nothing in panic or crash logs except this: 12/29/13 1:49:17.286 PM com.apple.launchd.peruser.501[294]: (com.apple.ReportCrash) Falling back to default Mach exception handler. Could not find: com.apple.ReportCrash.Self
Once I finally got in, I went to disk utiloity and ran verify permissions and saw many issues, then ran repair disk permissions.  I wanted to keep the log of all the changes and went to print and save as PDF - it was over 521 pages of permissions fixed! I didn't bother saving that file, I wish I did now.
I've been runing about 2 days without blue, gray crash so I am hoping that fixed it - but if this was a plane, no way would I fly it.
My question:  After the both reinstalls and clean installs, why would so many permissions need to be repaired?

For some reason, after I run repair permissions in Disk Utility, I can run it again, and the same problems are "corrected."
That's a waste of time.
Is Disk Utility actually doing anything?
Basically, nothing on second or subsequent runs when the function is used repeatedly.
It seems like every time I run repair permissions the same problems are present. Has this happened to anyone else?
Click here for information.
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