Disk permissions verfication not repairing all files

We Have Mac OS X Server 10.5.6 installed and we just ran Disk Utility to repair the permissions on the boot volume.
It repaired a lot of things on the first run, but not all. Below is the output of the second run:
+Verify permissions for “Leopard Server”+
+ Reading permissions database.+
+ Reading the permissions database can take several minutes.+
+ACL found but not expected on "private/var/db/openldap/openldap-data/DB_CONFIG.example".+
+ACL found but not expected on "Network".+
+Warning: SUID file "System/Library/Filesystems/AppleShare/afpLoad" has been modified and will not be repaired.+
+Warning: SUID file "usr/bin/setregion" has been modified and will not be repaired.+
+Warning: SUID file "System/Library/PrivateFrameworks/Install.framework/Versions/A/Resources/runner " has been modified and will not be repaired.+
+Warning: SUID file "System/Library/Printers/IOMs/LPRIOM.plugin/Contents/MacOS/LPRIOMHelper" has been modified and will not be repaired.+
+ACL found but not expected on "Library/WebServer".+
+Permissions verification complete+
What can I do to fix these errors? Thanks!

Thanks for the reply's!
I did run 'Check permissions' first, after that I ran 'Fix permissions' two times.
The output I posted above was indeed the output of a 'Check' run. But this was just to see what wasn't fixed after the to 'Fix' runs.
To reboot the server with the installation CD sounded very logical (why didn't I think of that). I just tried it, and a lot of things were fixed. After that I ran the check again, this is the output:
*Output of 'Check Permissions' after a 'Fix permissions', (both from the 10.5 Server CD):*
+ACL found but not expected on "private/var/db/openldap/openldap-data/DB_CONFIG.example".+
+ACL found but not expected on "Network".+
+Warning: SUID file "System/Library/Filesystems/AppleShare/afpLoad" has been modified and will not be repaired.+
+Warning: SUID file "usr/bin/setregion" has been modified and will not be repaired.+
+Warning: SUID file "System/Library/PrivateFrameworks/Install.framework/Versions/A/Resources/runner " has been modified and will not be repaired.+
+Warning: SUID file "System/Library/Printers/IOMs/LPRIOM.plugin/Contents/MacOS/LPRIOMHelper" has been modified and will not be repaired.+
+ACL found but not expected on "Library/WebServer".+
+Permissions verification complete+
Still a lot of un-fixed things.... What can I do?

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    Best Wish
    ACATISNOTACAT

    Hey im having the same problem, heres what mine says, Just want to check and see if the same thing to be on the safe side.
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    Repairing permissions for “Mikey HD”
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    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/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/Java/Support/VisualVM.bundle/Contents/Home/profiler3/lib/deploy ed/jdk15/hpux-pa_risc2.0/libprofilerinterface.sl", should be -rw-r--r-- , they are -rwxr-xr-x .
    Repaired "System/Library/Java/Support/VisualVM.bundle/Contents/Home/profiler3/lib/deploy ed/jdk15/hpux-pa_risc2.0/libprofilerinterface.sl".
    Permissions differ on "System/Library/Java/Support/VisualVM.bundle/Contents/Home/profiler3/lib/deploy ed/jdk15/hpux-pa_risc2.0w/libprofilerinterface.sl", should be -rw-r--r-- , they are -rwxr-xr-x .
    Repaired "System/Library/Java/Support/VisualVM.bundle/Contents/Home/profiler3/lib/deploy ed/jdk15/hpux-pa_risc2.0w/libprofilerinterface.sl".
    Permissions differ on "System/Library/Java/Support/VisualVM.bundle/Contents/Home/profiler3/lib/deploy ed/jdk16/hpux-pa_risc2.0/libprofilerinterface.sl", should be -rw-r--r-- , they are -rwxr-xr-x .
    Repaired "System/Library/Java/Support/VisualVM.bundle/Contents/Home/profiler3/lib/deploy ed/jdk16/hpux-pa_risc2.0/libprofilerinterface.sl".
    Permissions differ on "System/Library/Java/Support/VisualVM.bundle/Contents/Home/profiler3/lib/deploy ed/jdk16/hpux-pa_risc2.0w/libprofilerinterface.sl", should be -rw-r--r-- , they are -rwxr-xr-x .
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    Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jce.jar".
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    Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jconsole.jar ".
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    Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/management-a gent.jar".
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    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".
    Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
    Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/VisualVM.bundl e/Contents/Home/profiler3/lib/deployed/jdk15/hpux-pa_risc2.0/libprofilerinterfac e.sl", should be -rwxr-xr-x , they are -rw-r--r-- .
    Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/VisualVM.bundl e/Contents/Home/profiler3/lib/deployed/jdk15/hpux-pa_risc2.0/libprofilerinterfac e.sl".
    Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/VisualVM.bundl e/Contents/Home/profiler3/lib/deployed/jdk15/hpux-pa_risc2.0w/libprofilerinterfa ce.sl", should be -rwxr-xr-x , they are -rw-r--r-- .
    Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/VisualVM.bundl e/Contents/Home/profiler3/lib/deployed/jdk15/hpux-pa_risc2.0w/libprofilerinterfa ce.sl".
    Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/VisualVM.bundl e/Contents/Home/profiler3/lib/deployed/jdk16/hpux-pa_risc2.0/libprofilerinterfac e.sl", should be -rwxr-xr-x , they are -rw-r--r-- .
    Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/VisualVM.bundl e/Contents/Home/profiler3/lib/deployed/jdk16/hpux-pa_risc2.0/libprofilerinterfac e.sl".
    Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/VisualVM.bundl e/Contents/Home/profiler3/lib/deployed/jdk16/hpux-pa_risc2.0w/libprofilerinterfa ce.sl", should be -rwxr-xr-x , they are -rw-r--r-- .
    Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/VisualVM.bundl e/Contents/Home/profiler3/lib/deployed/jdk16/hpux-pa_risc2.0w/libprofilerinterfa ce.sl".
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