Same here. But without knowing for sure why Apple did let this messages appear, in short, you should consider them as not important...at least for now...and here is why for the ones interested in some details about the error:
Permissions differ on “Applications/iTunes.app/Contents/Resources/Dutch.lproj/AACEncoderConfig.nib”; should be drwxr-xr-x ; they are -rwxr-xr-x .
What this means in Unix language is that permissions check is expecting that "AACEncoderConfig.nib" to be a directory and it's not. You can tell because of "drwxr-xr-x" the d letter at the beginning of the string means "directory" and when compared with the actual value "-rwxr-xr-x", the absence of d means that it refers to a file.
Now you might ask why is the system expecting a directory?
Here is a link that describes why: http://support.apple.com/kb/HT1452?viewlocale=en_US&locale=en_US
OK...but what is this kind of files .nib?
This files are normally GUI files...and in the past...not so far away...it was based on a directory structure...but iTunes 11.1 is the first released Apple app that is using their new nib file spec. And this is somehow apparent...I mean the error messages we are all seeing when we run the permissions check suggest it.
Then I need to add, as a guess, it looks like this is due to the coming OSX upgrade...I saw another software giving the same permissions errors and even if I cannot say which app, it's one that is heavily tested right now and it will appear on OSX Lion/Mountain Lion and the new Mavericks.
Hope this helps!
I have opened a bug report at https://bugreport.apple.com/
The number is 15037979 so you can open a bug too and refer to this case.