I am having a problem using Xcode 5 that might be the same issue. ibtools is randomly working when generating or writing localized strings to/from xib files. I had to use sudo on some xib files to get it to work.
Here's an example:
$ibtool --generate-strings-file en.lproj/MyVC.strings en.lproj/MyVC.xib
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN"
"http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>com.apple.ibtool.errors</key>
<array>
<dict>
<key>description</key>
<string>Interface Builder could not open the document "MyVC.xib" because it does not exist.</string>
</dict>
</array>
</dict>
</plist>
Using sudo works although it complains about 'user domains will be volatile'
$sudo ibtool --generate-strings-file en.lproj/MyVC.strings en.lproj/MyVC.xib
2013-10-01 10:04:35.943 Interface Builder Cocoa Touch Tool[1717:303] CFPreferences: user
home directory at file:///var/root/Library/Application%20Support/iPhone%20Simulator/User/ is unavailable. User domains will be volatile.
$