I always use iTunes for ripping CDs to AIF and have never once had a problem with taking the newly created files and messing around with them in Amadeus or SoundEdit or FinalCutPro or anything else for that matter.
Stupid comment probably, but make sure the files aren't locked. Find the files through the Finder and Show Info to see if the Locked checkbox is activated.
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I always use iTunes for ripping CDs to AIF and have never once had a problem with taking the newly created files and messing around with them in Amadeus or SoundEdit or FinalCutPro or anything else for that matter.