Just repaired and verified permissions -- what are these that aren't fixed?

[MythicFrost]

Hey,

I've just repaired permissions on my Mac (many were fixed), and then verified them, these aren't fixed though:

Verify permissions for “Macintosh HD”
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/Contents/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/deploy.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/deploy.jar", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/libdeploy.jnilib", should be -rwxr-xr-x , they are lrwxr-xr-x .
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent" has been modified and will not be repaired.

Permissions verification complete

Any idea's why? And is any of this an issue? Oh, just out of curiosity why does it say "they are lrw-r--r--" what does that stand for?

EDIT: I repaired again (and it said it repaired the JavaVM ones, all three of them), and verified again and this is the result:

Verify permissions for “Macintosh HD”
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/Contents/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/deploy.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/deploy.jar", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/libdeploy.jnilib", should be -rwxr-xr-x , they are lrwxr-xr-x .
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent" has been modified and will not be repaired.

Permissions verification complete

They look identical.

 

[FourCandles]

This is presumably because OS X has updated the file whilst your Repair Permissions scan was running. According to Apple, it can be ignored:

http://support.apple.com/kb/TS1448

 

[MythicFrost]

This is presumably because OS X has updated the file whilst your Repair Permissions scan was running. According to Apple, it can be ignored:

http://support.apple.com/kb/TS1448

Ah, thank you. What about the JavaVM messages?

 

[FourCandles]

Ah, thank you. What about the JavaVM messages?

I wouldn't worry too much about any Java permission errors, they come up all the time in Repair Permissions.
EDIT: better explanation by belvdr below

Oh, and lrw-r--r-- etc. is a symbolic representation of the UNIX (the underlying base of OS X) file permissions themselves.

 

[belvdr]

Those are symlinks. Repair permissions uses chmod which, without the -h flag, modifies the original file, not the symlink itself.

 

[MythicFrost]

Ah thanks very much guys!