Launch Extension Manager again as administrator and do the operation again.
Windows: Right click Extension Manager and select "Run as administrator" in the context menu.
Mac: Run Extension Manager with "sudo" command, for example, for Extension Manager CS5.5, you can run the command below in terminal.
sudo "/Applications/Adobe Extension Manager CS5.5/Adobe Extension Manager CS5.5.app/Contents/MacOS/Adobe Extension Manager CS5.5"