The disk permissions issue is a common issue. Certain files never really get fixed. If you want to double check... what files is Disk Utility reporting with the wrong permissions?
Yesterday it was just a few files, today it's a whole string of them, and this is after a repair.
===== Sunday, May 12, 2013 7:16:04 PM Eastern Daylight Time =====
2013-05-12 19:16:08 -0400: Verifying permissions for Macintosh HD
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/Dutch.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/French.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/German.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/Italian.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/Japanese.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/da.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/fi.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/hr.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/ko.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/no.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/pl.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/pt.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/pt_PT.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/ru.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/sk.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/sv.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/zh_CN.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:11 -0400: Permissions differ on System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resources/zh_TW.lproj/DisplaysPref.nib; should be -rw-r--r-- ; they are -rwxr-xr-x .
2013-05-12 19:16:13 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane; should be drwxr-xr-x ; they are lrwxr-xr-x .
2013-05-12 19:16:28 -0400: Permissions differ on System/Library/CoreServices/Menu Extras/Displays.menu; should be drwxr-xr-x ; they are lrwxr-xr-x .
2013-05-12 19:16:33 -0400: Permissions differ on System/Library/MonitorPanels/Arrange.monitorPanel; should be drwxr-xr-x ; they are lrwxr-xr-x .
2013-05-12 19:16:33 -0400: Permissions differ on System/Library/MonitorPanels/Display.monitorPanel; should be drwxr-xr-x ; they are lrwxr-xr-x .
2013-05-12 19:16:33 -0400: Permissions differ on System/Library/MonitorPanels/Profile.monitorPanel; should be drwxr-xr-x ; they are lrwxr-xr-x .
2013-05-12 19:16:33 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/hr.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:33 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/sk.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:40 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/pl.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:41 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/pt_PT.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:42 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/zh_TW.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:42 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/zh_CN.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:43 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/pt.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:44 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/sv.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:45 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/ru.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:45 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/no.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:46 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/ko.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:47 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/fi.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:48 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/da.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:49 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/Dutch.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:49 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/Italian.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:51 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/French.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:52 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/German.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:16:53 -0400: Permissions differ on System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/Japanese.lproj/DisplaysPref.nib; should be drwxr-xr-x ; they are -rwxr-xr-x .
2013-05-12 19:17:19 -0400:
2013-05-12 19:17:19 -0400: Permissions verification complete
2013-05-12 19:17:19 -0400:
2013-05-12 19:17:19 -0400: