Martin,
Under iTunes>Preferences, your "use sound check" was checked off. What it does is determine the volume of your music in order to keep a uniform volume level across tracks. Sounds like you started off importing music to your external with this option unchecked and then at some time checked it off. When you connected your external and iTunes recognized tracks that had not been "normalized" it did so for you. Now that it has been done for the entirety of your library, iTunes functions normally.
So long as your music sounds fine, I think everything will be ok.
hope this helps