How do I fix this disk permission problem?

I use Disk Utility frequently. My iMac was shipped by a friend and got jostled so I rarely restart the machine. The internal DVD drive stopped working. I bought an external DVD drive that works fine. I was afraid the motherboard might be the problem, not the internal drive itself. Since getting the machine, I did a clean install of Snow Leopard. Everything seems to be working fine but when I use Disk Utility this always happens- I have lots of wrong disk permissions, always the same ones. It takes about 15 minutes to do a whole scan. Here is what it shows- all having to do with Java- and the final problem is always the same-"Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired":
Can someone tell me what I can do to fix this?
Thank you
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/dt.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/dt.jar".
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jce.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jce.jar".
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".
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/management- agent.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/management- agent.jar".
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".
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/dt.jar", should be -rw-r--r-- , they are -rwxr-xr-x .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/dt.jar".
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/jce.jar", should be -rw-r--r-- , they are -rwxr-xr-x .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/jce.jar".
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/management -agent.jar", should be -rw-r--r-- , they are -rwxr-xr-x .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/management -agent.jar".
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/security/b lacklist", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/security/b lacklist".
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/Home/lib/security/cacerts", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/Support/Deploy.bundle/Contents/Home/lib/security/cacerts".
Permissions differ on "System/Library/Java/Support/Deploy.bundle/Contents/Resources/Java/deploy.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Java/Support/Deploy.bundle/Contents/Resources/Java/deploy.jar".
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/dt.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/dt.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jce.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jce.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 ".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/management-a gent.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/management-a gent.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".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/dt.jar", should be lrwxr-xr-x , they are -rw-r--r-- .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/dt.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/jce.jar", should be lrwxr-xr-x , they are -rw-r--r-- .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/jce.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/management- agent.jar", should be lrwxr-xr-x , they are -rw-r--r-- .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/management- agent.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/security/bl acklist", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/security/bl acklist".
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", should be drwxr-xr-x , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle".
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".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Home/lib/security/cacerts", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Home/lib/security/cacerts".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Resources/Java/deploy.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Resources/Java/deploy.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Resources/Java/libdeploy.jnilib", should be -rwxr-xr-x , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Resources/Java/libdeploy.jnilib".
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.

Those messages are routine.  See this Apple document.

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