Same here. Permissions on /Users are set to 777 after the OS X 10.9.3 upgrade (and I believe the group should also be wheel?!). While "Disk Utility" detects and repairs this, permissions are reset to 777 after each reboot:
drwxrwxrwx@ 7 root admin 238 15 May 20:14 Users
After each and every reboot, "Disk Utility" finds this:
Verifying permissions for “Macintosh HD”
Permissions differ on “Applications/Safari.app/Contents/Resources/Safari.help/Contents/Resources/inde x.html”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Permissions differ on “Users”; should be drwxr-xr-x ; they are drwxrwxrwx .
Permissions differ on “Users/Shared”; should be drwxrwxrwt ; they are drwxrwxrwx .
Permissions verification complete
I do not think my system is heavily modified:
Tims-MacBook-Pro:~ tim$ kextstat | grep -v com.apple
Index Refs Address Size Wired Name (Version) <Linked Against>
Tims-MacBook-Pro:~ tim$ ls -l /Library/LaunchDaemons/
total 32
-rw-r--r-- 1 root wheel 462 18 Apr 15:46 com.adobe.fpsaud.plist
-rw-r--r-- 1 root wheel 568 2 Apr 2012 com.microsoft.office.licensing.helper.plist
lrwxr-xr-x 1 root wheel 103 18 Feb 20:59 com.oracle.java.Helper-Tool.plist -> /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Resources/com.oracle.java.Helper-Tool .plist
-rw-r--r-- 1 root wheel 486 22 Apr 20:59 com.oracle.java.JavaUpdateHelper.plist
Tims-MacBook-Pro:~ tim$ ls -l /Library/LaunchAgents/
total 8
lrwxr-xr-x 1 root wheel 104 18 Feb 20:59 com.oracle.java.Java-Updater.plist -> /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Resources/com.oracle.java.Java-Update r.plist
Tims-MacBook-Pro:~ tim$ ls -l /Library/LaunchDaemons/
total 32
-rw-r--r-- 1 root wheel 462 18 Apr 15:46 com.adobe.fpsaud.plist
-rw-r--r-- 1 root wheel 568 2 Apr 2012 com.microsoft.office.licensing.helper.plist
lrwxr-xr-x 1 root wheel 103 18 Feb 20:59 com.oracle.java.Helper-Tool.plist -> /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Resources/com.oracle.java.Helper-Tool .plist
-rw-r--r-- 1 root wheel 486 22 Apr 20:59 com.oracle.java.JavaUpdateHelper.plist
Tims-MacBook-Pro:~ tim$