You ask many questions but the key to all this is the message at the end of the repair process. If it suggests the repair is completed, it is completed. You can ignore any warnings. Sometimes these 'faults' are symptoms of Apple work in progress that will eventually be resolved through an update.
The matter of whether you should turn off your machine is debatable but usually the general opinion is that you need only turn off your machine if you are going away for an extended period. Its use of power is minimal if that is what troubles you.
As long as the report ends up with 'Permissions repair complete' then, as far as permissions go, you are fine. You can ignore the various statements in the report:
Permissions you can ignore on 10.5 onwards:
Using 'should be -rw-r--r-- , they are lrw-r--r--' as an example, you will see the that the permissions are not changed, but the | indicates a different location. This is because an update to Leopard onwards changed the location of a number of system components.
Poster rccharles has provided this description of what it all means:
d = directory
r = read
w = write
x = executeable program
| | |
| | all other users not in first two types
a little more info
Before the user had read & write. A member of the group had read.
After, only the user had read & write.
I have repaired the disk permissions but can anyone suggest why is this happening?
The original RemoteDesktopMenu.nib was delivered by the package com.apple.MacOSX.lang.es. It was the old style nib (next interface builder), a directory containing a nib file. The package com.apple.pkg.RemoteDesktopClient delivered the nib file in the new format, a single Apple binary plist. Nothing to worry about.