Repair permissions does not seem to repair them

As I have sleep problems (energy Saver settings do not kick in when they should) that I am trying to fix for a time now
To fix, I ran permission repair again. I than tried to run it again as it found a bunch of things to repair. After it finished it gives me exactly the same list of the same faults. Run it again and ditto.
Is this normal?
Here the list for your information, and while we at it do you see anything that could cause my sleep problem?
Repairing permissions for “OS”
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jconsole.ja r", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jconsole.ja r".
User differs on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib", should be 0, user is 95.
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib".
User differs on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries", should be 0, user is 95.
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries".
Permissions differ on "System/Library/Java/Support/Deploy.bundle/Contents/Resources/JavaPluginCocoa.b undle/Contents/Resources/Java/deploy.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/Support/Deploy.bundle/Contents/Resources/JavaPluginCocoa.b undle/Contents/Resources/Java/deploy.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jconsole.jar ", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jconsole.jar ".
User differs on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib", should be 95, user is 0.
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib".
User differs on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries", should be 95, user is 0.
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/deploy.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/deploy.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/libdeploy.jnilib", should be -rwxr-xr-x , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/libdeploy.jnilib".
ACL found but not expected on "private/var/root".
Repaired "private/var/root".
ACL found but not expected on "private/var/root/Library".
Repaired "private/var/root/Library".
ACL found but not expected on "private/var/root/Library/Preferences".
Repaired "private/var/root/Library/Preferences".
Permissions repair complete

I have been on the phone with Apple and, well lets say, get a polite reinstall the OS software, must be an other application and all the other answers you get when they do not know.
Good to hear I am not alone. We have 2 MBP's and both have it.
I am using PleaseSleep, (http://www.dragonone.com/products/macosx/pleasesleep/) and it helps bit.
I have ben trying and testing for 3 weeks now, and am not able to recreate the problem, and as such suspect indeed it is the OS and not the the software I sue. Otherwise it should always not sleep after or while I run application XYZ.
Love to hear creative thoughts.

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Repair permissions will not complete the repairs

When I repair permissions I get the following no matter how many times I try.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Reading permissions database.
Reading the permissions database can take several minutes.
Permissions differ on "sbin/restore", should be -r-xr-xr-x , they are -r-sr-sr-x .
Warning: SUID file "sbin/restore" has been modified and will not be repaired.
Permissions differ on "sbin/rrestore", should be -r-xr-xr-x , they are -r-sr-sr-x .
Warning: SUID file "sbin/rrestore" has been modified and will not be repaired.
Permissions differ on "sbin/mount_smbfs", should be -r-xr-xr-x , they are -r-sr-xr-x .
Warning: SUID file "sbin/mount_smbfs" has been modified and will not be repaired.
Permissions differ on "usr/bin/smbutil", should be -r-xr-xr-x , they are -r-sr-xr-x .
Warning: SUID file "usr/bin/smbutil" has been modified and will not be repaired.
Permissions repair complete
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Any suggestions?
Harold

Thanks for responding V.K.,
I am not familiar with running terminal commands but am anxious to do so.
Let me add a little info that may help decipher my problem.
I had a problem prior to repairing permissions as follows.
Startup was taking about 7 minutes.
When starting it would give Apple logo with spinning bars longer than usual. Then it would delay as if locked up on the blank white screen. Then open normally. However it locked up on variety of apps and at times the curser would not function from either the mouse or the touchpad. I also noticed that some keys would not function either from the computer keyboard or the Apple wireless keyboard. The space bar was one inoperable key and the ‘e’ & ‘n’ keys.
I ran DiskWarrier and it showed 20% fragmentation. I have never seen more than 4% in many years with Macs. After clearing the fragmenting back to '0' I checked all files, etc.
I then ran repair permissions which showed many in need of repair but no help on startup. I then reset PRAM. After resetting it cleared up the slow startup but the permissions are persistant.
And that is when I turned to discussions for help.
Having to do with user ID I wonder if it could be from outside my home??
I have a secure network password protected using AirPort 'n' series.
Harold

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Elaine, did you change your name from Andy, or are you a separate person? Most of us don't pay that close attention to the name and since your response seemed to be a continuation of Andy's problem, nobody noticed.
Your question appeared to show absolutely no attempt to try the solutions provided for Andy (who we thought you were). What you did is called "threadjacking," and you did it in a way that made everyone believe you were actually Andy, who's thread you threadjacked.
Being that you are a self-professed novice, here's a very basic thing you need to understand: for the most part, data is separate from applications. So, just because your application (Word in this case) no longer works, that doesn't mean your documents are in jeopardy. You can install Office (Word) 2008 or 2011 and open those documents just fine. You can also use any of the programs mentioned to open those documents. There is nothing to "merge" between the applications.
To move them to your new computer, just copy the documents to an external hard drive, thumb drive, or CD/DVD. You can then move them to your Macbook. You can also turn on file sharing and move them that way, but you probably ought to have a backup since you claim them to be important.
Do you have a backup of your iMac? If not, I would suggest getting an external drive copying all your data onto that, make sure it all reads ok, then do what you need to do with your iMac.
Apple's setup assistant should have asked if you wanted to move stuff from your old computer to your new one, which would have been the best way to do that; however, since it appears you have already set up your account on the new Mac, I'd just back up the iMac, either by straight copy, Carbon Copy Cloner, or SuperDuper. You can then move the files you want onto your new Mac from the external hard drive.

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Well!
If you have ThunderBolt, I would go with such for an External Working Drive, spinning platter or SSD depending on your budget
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Repair disk permissions does not work

Repair disk permissions does not work. Disk Uitliy fines many incorrect permissions (ACL found, but not expected) and says that it would repair it. However, when checked again, it finds the same permission errors.
I have tried Disk Utility as well as the command line "sudo diskutil repairPermissions /" (which probably does exactly the same as Disk Utility).
Any hints?
C.

Are you trying to Repair Permissions because you have file access problems in the System files, or just because you think you need to do it?
If the former, please explain what you are seeing. If the latter, stop wasting your time.
The things it doesn't repair are not repaired because there is nothing broken. The orginal Receipts files have the old settings, and subsequent updates have changed the permissions on those things to what they should be, now. It will report the differences it finds every time you run Repair Permissions because they will always be different and they should be the way they are.

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The good thing about mac-centric resellers such as OWC, is they have people on staff that can answer questions without you buying things first. They also have how-to information, and instructions are included in many of their products. I saw a link to watch a DIY video in one of their pages; an example of a RAID (with its own power supply) is shown on their drives page. Also a few in there, with no power supplies, for less money.
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Some ideas on the RAID backup methods appear in google search, some of the pages are ideas and concepts; and the better ones also warn about using RAID for the only backup plan.
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My backup method is not automatic, or a moving backup plan, if I don't get a move-on and make full system clones. I do make copies of photos and documents the manual way, to USB external drives; and occasionally backup to DVD or CD media. And USB flash, that helps to move files between computers without need to use file sharing via wi-fi. {Like Why fly? Walking is better exercise unless one is a bird. Squawk!}
https://www.google.com/#q=raid+backup+mac
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My ideas would not be all that interesting to follow as a backup
plan when matching available newer hardware to task, but you
can get some into better ideas if you are not in a rush. Get a
good setup and then look into more an betterer stuff.
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Repair permissions does not seem to repair them

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